From paul.bauer.q at gmail.com  Wed Jan  1 18:09:34 2020
From: paul.bauer.q at gmail.com (Paul bauer)
Date: Wed, 01 Jan 2020 17:09:34 -0000
Subject: [gmx-users] GROMACS 2020 official release
Message-ID: <f7408a41-9e20-52aa-1220-310723cc46cc@gmail.com>

Hello GROMACS users!

The official release of GROMACS 2020 is now available.

What new things can you expect? Please see the release notes highlights at
http://manual.gromacs.org/2020/release-notes/index.html.

You can find the code, manual, release notes, installation instructions and
test suite at the links below.

Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2020.tar.gz
Documentation: http://manual.gromacs.org/2020/index.html
(includes install guide, user guide, reference manual, and release notes)
Test Suite: http://gerrit.gromacs.org/download/regressiontests-2020.tar.gz

Happy simulating!

-- 
Paul Bauer, PhD
GROMACS Development Manager
KTH Stockholm, SciLifeLab
0046737308594


From dorosh at ualberta.ca  Thu Jan  2 04:54:56 2020
From: dorosh at ualberta.ca (Lyudmyla Dorosh)
Date: Thu, 02 Jan 2020 03:54:56 -0000
Subject: [gmx-users] Need help with installation of Gromacs-2019.3 with
 Intell compilers
In-Reply-To: <CABJycMD1HkqOTvgikfsesRf+H+9Oo8cPWXU4E_0eUUNBY0iLiQ@mail.gmail.com>
References: <CADg3LA+Z449EhxF82Yf_0XUt7rxqk9U288ZP2mEPLFxV9ENXWg@mail.gmail.com>
	<a36f69e8-f8ac-83e1-5040-a28cd0673559@gmail.com>
	<CADg3LA+tupwUUqTn95cDuSS0x4hOXWB7+exctu5K1_1r_nZz5A@mail.gmail.com>
	<CABJycMD1HkqOTvgikfsesRf+H+9Oo8cPWXU4E_0eUUNBY0iLiQ@mail.gmail.com>
Message-ID: <CADg3LALB8MV+gvefO2eVc-E4BZZ4gp3v1ykY2bjtVV6vaTqkxg@mail.gmail.com>

Dear Rajib,

Originally I have made too many irreversible changes to my ubuntu trying to
fit requirements, including nvidia cuda and openMPI. Hence segmentation
fault and system started crushing in general. Since then I re-installed
Ununtu, Intel drivers and libraries, newest version of cmake.

Ubuntu 18.04.3 LTS
Intel? Parallel Studio XE 2019
gromacs-2018.8.tar.gz
 fftw-3.3.8.tar.gz
cmake-3.16.0-rc1-Linux-x86_64.tar.gz

Sourced Intel compilers:
source /opt/intel/bin/compilervars.sh intel64
source /opt/intel/impi/2019.5.281/intel64/bin/mpivars.sh
source /opt/intel/mkl/bin/mklvars.sh intel64

Runned cmake install using the flags:
sudo cmake .. -DBUILD_SHARED_LIBS=off -DGMX_FFT_LIBRARY=mkl
-DCMAKE_INSTALL_PREFIX=$installDir -DGMX_MPI=on -DGMX_OPENMP=on
-DGMX_CYCLE_SUBCOUNTERS=on -DGMX_GPU=off -DGMX_SIMD=SSE2
-DCMAKE_C_COMPILER="/opt/intel/bin/icc"
-DCMAKE_CXX_COMPILER="/opt/intel/bin/icpc" -DREGRESSIONTEST_DOWNLOAD=on

Now it works perfectly, performance just great.
Fantastic reply from Quin K - THANKS.
Hope it helps,
Lyudmyla


On Mon, Dec 30, 2019 at 7:15 AM Rajib Biswas <chemrajib at gmail.com> wrote:

> Dear Gromacs-Users,
>
> Is there any update on this issue? I have used the following flags for
> version 2019.3
>
> /apps/codes/cmake/3.15.4/bin/cmake ..
> -DCMAKE_INSTALL_PREFIX=/opt/gromacs/2019.3 -DGMX_FFT_LIBRARY=fftw3
> -DCMAKE_PREFIX_PATH=/apps/libs/fftw/3.3.8 -DBUILD_SHARED_LIBS=OFF
>  -DGMX_DOUBLE=ON -DGMX_SIMD=AVX2_256 -DCMAKE_C_COMPILER=mpiicc
> -DCMAKE_CXX_COMPILER=mpiicpc -DGMX_MPI=ON -DGMX_OPENMP=ON
> -DGMX_BUILD_MDRUN_ONLY=ON
>
> and getting compilation error which says:
>
> [ 58%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o
> icpc: error #10105:
> /apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom:
> core dumped
> icpc: warning #10102: unknown signal(-497903120)
> icpc: error #10106: Fatal error in
> /apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom,
> terminated by unknown
> compilation aborted for
> /storage/rajib/opt/gromacs-2019.3/src/gromacs/pulling/pullutil.cpp (code 1)
> make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o]
> Error 1
> make[2]: *** Waiting for unfinished jobs....
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> make: *** [all] Error 2
>
> Your help will be highly appreciated.
>
> Thanking you.
>
> With regards,
> Rajib
>
>
>
> On Wed, Oct 9, 2019 at 4:03 AM Lyudmyla Dorosh <dorosh at ualberta.ca> wrote:
>
> > I have tried this command line:
> > sudo cmake .. -DBUILD_SHARED_LIBS=OFF -DGMX_FFT_LIBRARY=mkl
> > -DCMAKE_INSTALL_PREFIX=$installDir -DGMX_MPI=ON -DGMX_OPENMP=ON
> > -DGMX_CYCLE_SUBCOUNTERS=ON -DGMX_GPU=OFF -DGMX_SIMD=SSE2
> > -DCMAKE_C_COMPILER="/home/doroshl/apps/intel/bin/icc"
> > -DCMAKE_CXX_COMPILER="/home/doroshl/apps/intel/bin/icpc"
> > -DREGRESSIONTEST_DOWNLOAD=ON
> > which had no errors for *cmake* or *make -j 4*, but *make check* gave me
> an
> > error:
> > ...
> > [100%] Running all tests except physical validation
> > Test project /home/doroshl/gromacs-2019.3/build
> >       Start  1: TestUtilsUnitTests
> >  1/46 Test  #1: TestUtilsUnitTests ..................***Failed    0.00
> sec
> > /home/doroshl/gromacs-2019.3/build/bin/testutils-test: error while
> loading
> > shared libraries: libmkl_intel_lp64.so: cannot open shared object file:
> No
> > such file or directory
> > ...
> > 0% tests passed, 46 tests failed out of 46
> >
> > so I included libmkl_intel_lp64.so:
> > sudo cmake .. -DBUILD_SHARED_LIBS=OFF -DGMX_FFT_LIBRARY=mkl
> > -DCMAKE_INSTALL_PREFIX=$installDir
> >
> >
> -DMKL_LIBRARIES="/home/doroshl/apps/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so"
> > -DMKL_INCLUDE_DIR="/home/doroshl/apps/intel/intelpython2/lib"
> > -DCMAKE_CXX_LINK_FLAGS="-Wl,-rpath,/usr/bin/gcc/lib64
> -L/usr/bin/gcc/lib64"
> > -DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_CYCLE_SUBCOUNTERS=ON -DGMX_GPU=OFF
> > -DGMX_SIMD=SSE2 -DCMAKE_C_COMPILER="/home/doroshl/apps/intel/bin/icc"
> > -DCMAKE_CXX_COMPILER="/home/doroshl/apps/intel/bin/icpc"
> > -DREGRESSIONTEST_DOWNLOAD=ON &> cmake.out
> > which doesn't give any error messages for cmake, but then in *sudo make
> -j
> > 4 *results in
> >
> > [ 46%] Building CXX object
> > src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o
> > icpc: error #10105:
> >
> >
> /home/doroshl/apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom:
> > core dumped
> > icpc: warning #10102: unknown signal(694380720)
> > icpc: error #10106: Fatal error in
> >
> >
> /home/doroshl/apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom,
> > terminated by unknown
> > compilation aborted for
> > /home/doroshl/gromacs-2019.3/src/gromacs/pulling/pullutil.cpp (code 1)
> > src/gromacs/CMakeFiles/libgromacs.dir/build.make:2136: recipe for target
> > 'src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o' failed
> > make[2]: ***
> [src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o]
> > Error 1
> > make[2]: *** Waiting for unfinished jobs....
> > CMakeFiles/Makefile2:2499: recipe for target
> > 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
> > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> > Makefile:162: recipe for target 'all' failed
> > make: *** [all] Error 2
> > Thanks for any help
> >
> >
> > On Tue, Oct 8, 2019 at 2:21 AM Paul bauer <paul.bauer.q at gmail.com>
> wrote:
> >
> > > Hej,
> > >
> > > I can't access the repository, so I can't say for certain what
> happened.
> > > Can you share your cmake command line?
> > >
> > > Cheers
> > >
> > > Paul
> > >
> > > On 07/10/2019 21:25, Lyudmyla Dorosh wrote:
> > > > Hello Gromacs Developers/Users,
> > > >
> > > > I'm trying to install Gromacs-2019.3 on Intel Xeon W-2175 with Intel
> > > > compilers (+MKL+MPI).
> > > > First I compiled cmake with Intel compilers. All output files are
> > > attached.
> > > > cmake, make seemed to go ok, but all check test failed. What do I do
> > > wrong?
> > > >
> > >
> >
> https://drive.google.com/file/d/1M8aOaq7ocmK4UOAzcRb5AqWMihIhVtmn/view?usp=sharing
> > > >
> > > > Thank you,
> > > >
> > > > Lyudmyla Dorosh, PhD
> > > > ------------------------------------------------------------
> > > > University of Alberta
> > > > Department of Electrical and Computer Engineering,
> > > > 4-021 ECERF
> > > > Edmonton, AB, T6G 2G8
> > > > Canada
> > > > Email: dorosh at ualberta.ca
> > > >
> > >
> > > --
> > > Paul Bauer, PhD
> > > GROMACS Release Manager
> > > KTH Stockholm, SciLifeLab
> > > 0046737308594
> > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> >
> >
> > --
> > Regards,
> >
> > Lyudmyla Dorosh, PhD
> > ------------------------------------------------------------
> > University of Alberta
> > Department of Electrical and Computer Engineering,
> > 4-021 ECERF
> > Edmonton, AB, T6G 2G8
> > Canada
> > Email: dorosh at ualberta.ca
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>


-- 
Regards,

Lyudmyla Dorosh, PhD
------------------------------------------------------------
University of Alberta
Department of Electrical and Computer Engineering,
4-021 ECERF
Edmonton, AB, T6G 2G8
Canada
Email: dorosh at ualberta.ca

From spss4 at iacs.res.in  Thu Jan  2 07:41:41 2020
From: spss4 at iacs.res.in (spss4 at iacs.res.in)
Date: Thu, 02 Jan 2020 06:41:41 -0000
Subject: [gmx-users] lifetime of hydrogen bond
Message-ID: <20200102121740.Horde.Exb1zPFlosEyzFm_w9xTmlG@mailweb.iacs.res.in>

Dear all
I want to calculate the hydrogen bond lifetime of a dynamic hydrogen  
bond which stays for say 10 ns (as I have saved the trajectory with 10  
ps interval).? I am trying to calculate the lifetime of this hydrogen  
bond by gmx hbond command
gmx hbond -f traj_nopbc.trr -s md.tpr -n index.ndx -num  
hbond_G4_N3_131_N3H4.xvg -dist dist_G4_N3_131_N3H4.xvg -ang  
ang_G4_N3_131_N3H4.xvg -life life_G4_N3_131_N3H4.xvg
Its give me a "uninterrupted hydrogen bond lifetime" plot which stays  
for 200 ps. I cannot understand the meaning of this plot. How to  
explain this 200 ps lifetime?
Thanks
sunipa?

From spoel at xray.bmc.uu.se  Thu Jan  2 08:28:23 2020
From: spoel at xray.bmc.uu.se (David van der Spoel)
Date: Thu, 02 Jan 2020 07:28:23 -0000
Subject: [gmx-users] lifetime of hydrogen bond
In-Reply-To: <20200102121740.Horde.Exb1zPFlosEyzFm_w9xTmlG@mailweb.iacs.res.in>
References: <20200102121740.Horde.Exb1zPFlosEyzFm_w9xTmlG@mailweb.iacs.res.in>
Message-ID: <4d21c8cc-068d-2cf5-e761-80b13e02df72@xray.bmc.uu.se>

Den 2020-01-02 kl. 07:47, skrev spss4 at iacs.res.in:
> Dear all
> I want to calculate the hydrogen bond lifetime of a dynamic hydrogen 
> bond which stays for say 10 ns (as I have saved the trajectory with 10 
> ps interval).? I am trying to calculate the lifetime of this hydrogen 
> bond by gmx hbond command
> gmx hbond -f traj_nopbc.trr -s md.tpr -n index.ndx -num 
> hbond_G4_N3_131_N3H4.xvg -dist dist_G4_N3_131_N3H4.xvg -ang 
> ang_G4_N3_131_N3H4.xvg -life life_G4_N3_131_N3H4.xvg
> Its give me a "uninterrupted hydrogen bond lifetime" plot which stays 
> for 200 ps. I cannot understand the meaning of this plot. How to explain 
> this 200 ps lifetime?
> Thanks
> sunipa
The -life option does not give you a meaningful answer since it is 
sensitive to small fluctuations. My oldpaper in J. Phys. Chem. B 110 pp. 
4393-4398 (2006) explains it in detail.

You can rerun without -life and with the -ac flag.

-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se

From spss4 at iacs.res.in  Thu Jan  2 09:11:17 2020
From: spss4 at iacs.res.in (spss4 at iacs.res.in)
Date: Thu, 02 Jan 2020 08:11:17 -0000
Subject: [gmx-users] lifetime of hydrogen bond
In-Reply-To: <4d21c8cc-068d-2cf5-e761-80b13e02df72@xray.bmc.uu.se>
References: <20200102121740.Horde.Exb1zPFlosEyzFm_w9xTmlG@mailweb.iacs.res.in>
	<4d21c8cc-068d-2cf5-e761-80b13e02df72@xray.bmc.uu.se>
Message-ID: <20200102133946.Horde.ACZBHvp283OKhveTEc-efk_@mailweb.iacs.res.in>

  Thank you for your suggestion.
----- Message from David van der Spoel <spoel at xray.bmc.uu.se> ---------
? ? Date: Thu, 2 Jan 2020 08:28:17 +0100
? ? From: David van der Spoel <spoel at xray.bmc.uu.se>
Reply-To: gmx-users at gromacs.org
Subject: Re: [gmx-users] lifetime of hydrogen bond
? ? ? To: gmx-users at gromacs.org

> Den 2020-01-02 kl. 07:47, skrev spss4 at iacs.res.in:
>> Dear all
>> I want to calculate the hydrogen bond lifetime of a dynamic  
>> hydrogen bond which stays for say 10 ns (as I have saved the  
>> trajectory with 10 ps interval).? I am trying to calculate the  
>> lifetime of this hydrogen bond by gmx hbond command
>> gmx hbond -f traj_nopbc.trr -s md.tpr -n index.ndx -num  
>> hbond_G4_N3_131_N3H4.xvg -dist dist_G4_N3_131_N3H4.xvg -ang  
>> ang_G4_N3_131_N3H4.xvg -life life_G4_N3_131_N3H4.xvg
>> Its give me a "uninterrupted hydrogen bond lifetime" plot which  
>> stays for 200 ps. I cannot understand the meaning of this plot. How  
>> to explain this 200 ps lifetime?
>> Thanks
>> sunipa
>
> The -life option does not give you a meaningful answer since it is  
> sensitive to small fluctuations. My oldpaper in J. Phys. Chem. B 110  
> pp. 4393-4398 (2006) explains it in detail.
>
> You can rerun without -life and with the -ac flag.
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
> --
> Gromacs Users mailing list
>
> * Please search the archive at  
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before  
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests  
> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or  
> send a mail to gmx-users-request at gromacs.org.

----- End message from David van der Spoel <spoel at xray.bmc.uu.se> -----

From j.su.vardhan at gmail.com  Thu Jan  2 12:11:35 2020
From: j.su.vardhan at gmail.com (Suvardhan Jonnalagadda)
Date: Thu, 02 Jan 2020 11:11:35 -0000
Subject: [gmx-users] Extract LJ-14 energy
In-Reply-To: <5f9ec346-3a77-91be-42c6-2c2e7ca827de@vt.edu>
References: <CAL7TV_i=YHtG9PfVDpiNU9TkdeM2uUWx4qgzO-OnBu8MLoYjcQ@mail.gmail.com>
	<CAM7TW5v6eiFPFJVJBuTa4BHFBsXqKuZhoUaxpK-WLD=-2kMN+Q@mail.gmail.com>
	<CAL7TV_i1WOp90KFSWusEK+iF=NoNj9-++U0VPqfNPAywFWwAjQ@mail.gmail.com>
	<5f9ec346-3a77-91be-42c6-2c2e7ca827de@vt.edu>
Message-ID: <CAL7TV_gWKCdQWWC0D=oBn1xvYvaovV0OWih8Qj2hWbY4BRm4CA@mail.gmail.com>

Hi,
Thanks for the reply. In the log file I could not find any 'LJ14' term, but
'LJ (SR) term is present.

My molecule has 17 atoms, and there are 1-4 interactions.

1.) Is the LJ(SR) term not the same as LJ14, in my case, since I have only
one molecule?

2.) Also, how to see what 1-4 interactions gromacs has considered for the
calculations? When I calculated for the molecule, manually, the 1-4 LJ
contribution is mismatching.

Sorry for late response.

Thanks and regards,

On Sat, 21 Dec, 2019, 7:04 AM Justin Lemkul, <jalemkul at vt.edu> wrote:

>
>
> On 12/20/19 6:07 AM, Suvardhan Jonnalagadda wrote:
> > Hi,
> > Thanks for the reply.
> > I have included it and rerun my system. Still problem prevails.
>
> energrps are not required for LJ 1-4 energies, as these are
> intramolecular and energygrps correspond strictly to intermolecular
> interaction energies.
>
> There is no need for enemat, which in any case is not practical to use
> enemat, just extract the energies with gmx energy. As Mark said, if your
> topology specifies 1-4 interactions, the energy contribution will be
> there. If it's not, there are no 1-4 interactions.
>
> -Justin
>
> >
> >
> > On Fri, 20 Dec, 2019, 7:22 AM Bratin Kumar Das, <
> 177cy500.bratin at nitk.edu.in>
> > wrote:
> >
> >> Hi
> >>     You have to mention energygrous in your .mdp file and rerun the
> >> simulation. The details you'll get in gromacs protein- ligand complex
> >> tutorial.
> >>
> >> On Thu 19 Dec, 2019, 11:11 PM Suvardhan Jonnalagadda, <
> >> j.su.vardhan at gmail.com> wrote:
> >>
> >>> Hi All,
> >>>
> >>> *"GROMACS: VERSION 4.5.5; Precision: single"*
> >>> I have performed an md simulation for 1 time step, on a single molecule
> >>> with 17 atoms. I want to calculate all the energies (angle, dihedrals,
> >>> bonds, 1-4 interactions), and compare. However, I am not able to get
> the
> >>> LJ-14 interactions energy from the '*.edr'* file. When i searched in
> the
> >>> manual, I came across *'gmx enemat'* command.
> >>> I gave the following command
> >>>
> >>> *'gmx enemat -f nvt_single.edr -groups groups.dat -lj14'*
> >>> In the groups.dat I have entered the molecule name (as in the *.itp
> >>> *file).
> >>>
> >>> So, the error and warnings I get after the above command are as
> follows:
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> *"   group 16WARNING! could not find group Coul-SR:C16-C16 (16,16)in
> >> energy
> >>> fileWARNING! could not find group LJ-SR:C16-C16 (16,16)in energy
> >>> fileWARNING! could not find group LJ-14:C16-C16 (16,16)in energy
> fileWill
> >>> select half-matrix of energies with 0 elementsLast energy frame read 0
> >>> time    0.000            Will build energy half-matrix of 17 groups, 0
> >>> elements, over 1 framesSegmentation fault (core dumped)   "*
> >>> Is this a bug? or am I missing something?
> >>> Also, what does 'LJ(SR)' term in the energies include? In my case, I
> have
> >>> only one molecule. So, what does this LJ short range include?
> >>>
> >>> Thank you,
> >>>
> >>> Best regards,
> >>> Vardhan
> >>> --
> >>> Gromacs Users mailing list
> >>>
> >>> * Please search the archive at
> >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >>> posting!
> >>>
> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>
> >>> * For (un)subscribe requests visit
> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >>> send a mail to gmx-users-request at gromacs.org.
> >>>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From sandro.wrzalek at fu-berlin.de  Thu Jan  2 13:26:46 2020
From: sandro.wrzalek at fu-berlin.de (Sandro Wrzalek)
Date: Thu, 02 Jan 2020 12:26:46 -0000
Subject: [gmx-users] Gromacs 2019 - Ryzen Architecture
Message-ID: <2f123e28-d6bb-4958-8eab-85f8a1158a14@fu-berlin.de>

Hi,

happy new year!

Now to my problem:

I use Gromacs 2019.3 and to try to run some simulations (roughly 30k 
atoms per system) on my PC which has the following configuration:

CPU: Ryzen 3950X (overclocked to 4.1 GHz)

GPU #1: Nvidia RTX 2080 Ti

GPU #2: Nvidia RTX 2080 Ti

RAM: 64 GB

PSU: 1600 Watts


Each run uses one GPU and 16 of 32 logical cores. Doing only one run at 
time (gmx mdrun -deffnm rna0 -gpu_id 0 -nb gpu -pme gpu) the GPU 
utilization is roughly around 84% but if I add a second run, the 
utilization of both GPUs drops to roughly 20%, while leaving logical 
cores 17-32 idle (I changed parameter gpu_id, accordingly).

Adding additional parameters for each run:

gmx mdrun -deffnm rna0 -nt 16 -pin on -pinoffset 0 -gpu_id 0 -nb gpu 
-pme gpu

gmx mdrun -deffnm rna0 -nt 16 -pin on -pinoffset 17 -gpu_id 1 -nb gpu 
-pme gpu

I get a utilization of 78% per GPU, which is nice but not near the 84% I 
got with only one run. In theory, however, it should come at least close 
to that utilization.

I suspect, the Ryzen Chiplet design as the culprit since Gromacs seems 
to prefer the the first Chiplet, even if two simultaneous simulations 
have the resources to occupy both. The reason for the 78% utilization 
could be because of overhead between the two Chiplets via the infinity 
band. However, I have no proof, nor am I able to explain why gmx mdrun 
-deffnm rna0 -nt 16 -gpu_id 0 & 1 -nb gpu -pme gpu works as well - seems 
to occupy free logical cores then.

Long story short:

Are there any workarounds to squeeze the last bit out of my setup? Is it 
possible to choose the logical cores manually (I did not found anything 
in the docs so far)?


Thank you for your help!


Best,

Sandro


From paul.bauer.q at gmail.com  Thu Jan  2 14:32:45 2020
From: paul.bauer.q at gmail.com (Paul bauer)
Date: Thu, 02 Jan 2020 13:32:45 -0000
Subject: [gmx-users] Gromacs 2019 - Ryzen Architecture
In-Reply-To: <2f123e28-d6bb-4958-8eab-85f8a1158a14@fu-berlin.de>
References: <2f123e28-d6bb-4958-8eab-85f8a1158a14@fu-berlin.de>
Message-ID: <44a30732-2788-f60e-ecca-58959a63dc19@gmail.com>

Hello,

we only added full detection and support for the newer Rizen chip-sets 
with GROMACS 2019.5, so please try if the update to this version solves 
your issue.
If not, please open an issue on redmine.gromacs.org so we can track the 
problem and try to solve it.

Cheers

Paul

On 02/01/2020 13:26, Sandro Wrzalek wrote:
> Hi,
>
> happy new year!
>
> Now to my problem:
>
> I use Gromacs 2019.3 and to try to run some simulations (roughly 30k 
> atoms per system) on my PC which has the following configuration:
>
> CPU: Ryzen 3950X (overclocked to 4.1 GHz)
>
> GPU #1: Nvidia RTX 2080 Ti
>
> GPU #2: Nvidia RTX 2080 Ti
>
> RAM: 64 GB
>
> PSU: 1600 Watts
>
>
> Each run uses one GPU and 16 of 32 logical cores. Doing only one run 
> at time (gmx mdrun -deffnm rna0 -gpu_id 0 -nb gpu -pme gpu) the GPU 
> utilization is roughly around 84% but if I add a second run, the 
> utilization of both GPUs drops to roughly 20%, while leaving logical 
> cores 17-32 idle (I changed parameter gpu_id, accordingly).
>
> Adding additional parameters for each run:
>
> gmx mdrun -deffnm rna0 -nt 16 -pin on -pinoffset 0 -gpu_id 0 -nb gpu 
> -pme gpu
>
> gmx mdrun -deffnm rna0 -nt 16 -pin on -pinoffset 17 -gpu_id 1 -nb gpu 
> -pme gpu
>
> I get a utilization of 78% per GPU, which is nice but not near the 84% 
> I got with only one run. In theory, however, it should come at least 
> close to that utilization.
>
> I suspect, the Ryzen Chiplet design as the culprit since Gromacs seems 
> to prefer the the first Chiplet, even if two simultaneous simulations 
> have the resources to occupy both. The reason for the 78% utilization 
> could be because of overhead between the two Chiplets via the infinity 
> band. However, I have no proof, nor am I able to explain why gmx mdrun 
> -deffnm rna0 -nt 16 -gpu_id 0 & 1 -nb gpu -pme gpu works as well - 
> seems to occupy free logical cores then.
>
> Long story short:
>
> Are there any workarounds to squeeze the last bit out of my setup? Is 
> it possible to choose the logical cores manually (I did not found 
> anything in the docs so far)?
>
>
> Thank you for your help!
>
>
> Best,
>
> Sandro
>

-- 
Paul Bauer, PhD
GROMACS Development Manager
KTH Stockholm, SciLifeLab
0046737308594


From jalemkul at vt.edu  Thu Jan  2 14:53:11 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Thu, 02 Jan 2020 13:53:11 -0000
Subject: [gmx-users] Extract LJ-14 energy
In-Reply-To: <CAL7TV_gWKCdQWWC0D=oBn1xvYvaovV0OWih8Qj2hWbY4BRm4CA@mail.gmail.com>
References: <CAL7TV_i=YHtG9PfVDpiNU9TkdeM2uUWx4qgzO-OnBu8MLoYjcQ@mail.gmail.com>
	<CAM7TW5v6eiFPFJVJBuTa4BHFBsXqKuZhoUaxpK-WLD=-2kMN+Q@mail.gmail.com>
	<CAL7TV_i1WOp90KFSWusEK+iF=NoNj9-++U0VPqfNPAywFWwAjQ@mail.gmail.com>
	<5f9ec346-3a77-91be-42c6-2c2e7ca827de@vt.edu>
	<CAL7TV_gWKCdQWWC0D=oBn1xvYvaovV0OWih8Qj2hWbY4BRm4CA@mail.gmail.com>
Message-ID: <07dfc302-6644-5612-9218-8734fda9c101@vt.edu>



On 1/2/20 6:11 AM, Suvardhan Jonnalagadda wrote:
> Hi,
> Thanks for the reply. In the log file I could not find any 'LJ14' term, but
> 'LJ (SR) term is present.
>
> My molecule has 17 atoms, and there are 1-4 interactions.
>
> 1.) Is the LJ(SR) term not the same as LJ14, in my case, since I have only
> one molecule?

They are different. Depending on how your topology was constructed, 
LJ(SR) may encompass LJ14, but they are not equivalent.

> 2.) Also, how to see what 1-4 interactions gromacs has considered for the
> calculations? When I calculated for the molecule, manually, the 1-4 LJ
> contribution is mismatching.

Use gmx dump on your .tpr file. 1-4 interactions are computed for 
topologies with nrexcl = 3 and defined [pairs]. If you did not do this, 
you have no 1-4 energy term, but it will be computed as part of LJ(SR) 
unless nrexcl > 3.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From deligkaris at gmail.com  Thu Jan  2 21:02:52 2020
From: deligkaris at gmail.com (Christos Deligkaris)
Date: Thu, 02 Jan 2020 20:02:52 -0000
Subject: [gmx-users] atom moved too far
In-Reply-To: <eb6b4386-8d1c-0a69-d59b-bde928a48d87@vt.edu>
References: <CAAHQ3wnYn0XapewAPd0RoAsC0HZLVJ_CjYU5bZOtDPd=u8aw4g@mail.gmail.com>
	<eb6b4386-8d1c-0a69-d59b-bde928a48d87@vt.edu>
Message-ID: <CAAHQ3wmpoDWc1BNT90XsEARLe9gV=AVCCejonzouFvOtXqefeA@mail.gmail.com>

thank you Justin.

I saw on your umbrella sampling tutorial how to implement the restraints
using the pull code.

The protocol I used is (if I understand correctly your question): The
energy minimization reached the cutoff for maximum force 1000 in 346 steps.
My NVT equilibration was 50,000 steps of dt = 0.002 and I used 8 NPT
equilibration calculations, each with 31,250 steps of dt=0.002 (total NPT
equilibration time 500ps) where I slowly decreased the position restraints
on DNA and the small molecule, as well as the harmonic restraint between
the two.
What are the best temperature coupling groups to use when we are not
certain whether the small molecule will spend the entire simulation period
physically bound to the macromolecule or whether it will become fully
solvated at some point? Is Macromolecule and Non-macromolecule the best
option since the small molecule will always (to a small or large extent)
interact with water (versus the Macromolecule_and_small_molecule and
everything else grouping option)?

Best wishes,

Christos Deligkaris, PhD
Assistant Professor of Physics, University of Southern Indiana
SC2220, 8600 University Blvd, Evansville IN, 47712
Office Phone: (812) 228-5056
www.deligkaris.org @DeligkarisGroup


On Mon, Dec 30, 2019 at 7:30 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/30/19 5:34 AM, Christos Deligkaris wrote:
> > dear all,
> >
> > While running my production run of a small molecule noncovalently bound
> to
> > DNA in water, I got the error:
> >
> > Step 8921600:
> >
> > Atom 20338 moved more than the distance allowed by the domain
> decomposition
> > (0.457738) in direction X
> >
> > distance out of cell 0.495788
> >
> > New coordinates:    3.304    4.938    2.969
> >
> > Old cell boundaries in direction X:    0.000    0.715
> >
> > New cell boundaries in direction X:    0.000    0.709
> >
> >
> > -------------------------------------------------------
> >
> > Program:     gmx mdrun, version 2018.1
> >
> > Source file: src/gromacs/domdec/domdec.cpp (line 4076)
> >
> > MPI rank:    0 (out of 12)
> >
> >
> > Fatal error:
> >
> > An atom moved too far between two domain decomposition steps
> >
> > This usually means that your system is not well equilibrated
> >
> > The error occured at about time=18 ns. I erased the output files,
> > resubmitted the calculation again from the beginning time=0 and in that
> > attempt the error appeared at about 16 ns. In both cases it was an atom
> of
> > a water molecule that moved too far.
> >
> > I read the "gromacs blow up" webpage and thought maybe the harmonic
> > intermolecular constraints I have on the cap base pairs are too strong
> for
> > the time step of 0.002 so I decreased the time step to 0.001ps and that
> > calculation is now at about 60 ns (still running). I also tried using
> only
> > 6 cores with a step of 0.002 (I used 12 cores in the two failed
> > calculations) and that calculation is now at time=50ns (still running).
> >
> > The energy minimization reached the cutoff for maximum force 1000 in 346
> > steps. My NVT equilibration was 50,000 steps of dt = 0.002 and I used 8
> NPT
> > equilibration calculations, each with 31,250 steps of dt=0.002 (total NPT
> > equilibration time 500ps) where I slowly decreased the position
> restraints
> > on DNA and the small molecule, as well as the harmonic restraint between
> > the two.
> >
> > I implemented the harmonic restraint between the small molecule-DNA and
> the
> > cap base pairs using the following in the topology (just showing one
> > example)
> >
> > [ intermolecular_interactions ]
> >
> > [ bonds ]
> >
> > 455     483      6       0.18564  200
>
> It is easier to use the pull code to perform the same operation, and is
> more likely to be compatible with domain decomposition.
>
> > For the production run, I use
> >
> > comm-mode = Linear
> >
> > nstcomm = 100
> >
> > comm-grps = System
> >
> >
> > cutoff-scheme = Verlet
> >
> > nstlist = 10
> >
> > coulombtype = PME
> >
> > rcoulomb = 1.2
> >
> > vdwtype = Cut-off
> >
> > vdw-modifier = Potential-shift
> >
> > rvdw = 1.2
> >
> > rvdw-switch = 0
> >
> > DispCorr = no
> >
> > tcoupl = nose-hoover
> >
> > nh-chain-length = 1
> >
> > nsttcouple = -1
> >
> > tc-grps = DNA_NNK Water_and_ions
> >
> > tau-t = 0.4 0.4
> >
> > ref-t = 300 300
> >
> > pcoupl = Parrinello-Rahman
> >
> > pcoupltype = isotropic
> >
> > tau-p = 1.0
> >
> > ref-p = 1.0
> >
> > refcoord-scaling = com
> >
> > constraints = h-bonds
> >
> > constraint-algorithm = lincs
> >
> > I believe SETTLES is included in the TIP3P topology by default so I am
> > using that also.
> >
> > I have run three 50 ns production runs of the small molecule in water
> > without any problems (NPT equilibration was done in 1 calculation for
> these
> > three).
> >
> > I was surprised that the two failed calculations did not fail at exactly
> > the same time step (start with same positions, velocities and solve
> > determinist equations of motion).
>
> Domain decomposition and other optimizations introduce small
> differences, so you should not expect different runs to behave
> identically, even with the same .tpr file.
>
> > The error message suggests that the system was not well equilibrated.
> > Should I try doing my NPT equilibrations over 1 ns instead of 500ps?
>
> What has been your preparation protocol so far?
>
> > Is it possible that using as a temperature coupling group the
> > macromolecule-small molecule results in the blow up if the small molecule
> > ends up leaving the macromolecule? (I did see the small molecule becoming
> > fully solvated at some point in the trajectory of the failed
> calculations)
> >
> > Using a force constant of 200 kJ/mol/nm is perhaps too large for a time
> > step of 0.002 ps? (I think I tried removing the harmonic restraints
> between
> > the two bases on the cap base pairs and that calculation also failed).
> And
> > I have seen in the literature a time step of 0.002 ps is reasonable for
> DNA
> > and DNA-ligand calculations.
> >
> > It is not clear to me why using less cores allows the calculation to
> > proceed (unless it got to 50ns by chance and it will blow up eventually).
>
> Probably because with fewer cores you are not using domain
> decomposition, which points to some kind of incompatibility with your
> use of [intermolecular_interactions] and domain decomposition. If you
> really need some kind of restraint, try the pull code or merge the DNA
> chains into a single topology and apply a simple distance restraint.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From yogesh.rma13 at gmail.com  Thu Jan  2 21:58:00 2020
From: yogesh.rma13 at gmail.com (Yogesh Sharma)
Date: Thu, 02 Jan 2020 20:58:00 -0000
Subject: [gmx-users] molecule breakage during minimization
Message-ID: <CACWq+69F+AMqWkDr2XPEpNaU72=KsxNbg3wtLyt1091Ze6V2hw@mail.gmail.com>

Hello everyone,
Before equillibriation I was trying to minimize my protein membrane system.
energyminimized.gro file  when vizualized in vmd showed few lipid molecules
broken. Is it safe to use trjconv to make whole molecule after em or i can
proceed with breakage? This is the minimization.mdp file I am using
define                  = -DREST_ON -DSTEP6_0
integrator              = steep
emtol                   = 1000.0
nsteps                  = 5000
nstlist                 = 10
cutoff-scheme           = Verlet
rlist                   = 1.2
vdwtype                 = Cut-off
vdw-modifier            = Force-switch
rvdw_switch             = 1.0
rvdw                    = 1.2
coulombtype             = pme
rcoulomb                = 1.2
;
constraints             = h-bonds
constraint_algorithm    = LINCS

From yepingsun80 at gmail.com  Fri Jan  3 02:14:14 2020
From: yepingsun80 at gmail.com (Sun Yeping)
Date: Fri, 03 Jan 2020 01:14:14 -0000
Subject: [gmx-users] What is the "gen-vel" used for?
In-Reply-To: <91200d3b-d3d0-d909-dac1-33589f5ca1ae@vt.edu>
References: <6013cc34-2bd1-4dc3-912f-06d0f63e7c27.sunyeping@aliyun.com>
	<ec2fbb96-235f-98d9-ca6f-cb1bf81d75de@vt.edu>
	<852cf0ed-e2b1-4c59-8fc2-03955f8a60ab.sunyeping@aliyun.com>
	<91200d3b-d3d0-d909-dac1-33589f5ca1ae@vt.edu>
Message-ID: <CAJOhvFmrhZfEGbiAq_7dhkgv5t_4-UR5rHuH=S_qgqL7r4z9fg@mail.gmail.com>

On Tue, Dec 31, 2019 at 12:22 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/30/19 11:11 PM, sunyeping wrote:
> > Hello Justin,
> >
> > Thank you for your reply.
> >
> > If I need to prove the repeatability of a phenonmenon (such as the
> > peptide folding pathway or a conformational transition) in
> > simulations, is it reasonable to run the production MD several times
> > and each time the simulation is continued for the same NPT
> > equilibration? Do I need to introduce centain random factors (if not
> > the velocity) in each production simulation?
> >
>
> No, because those aren't independent observations. You're just running
> the same .tpr file over and over again, which will diverge slightly for
> numerical reasons but these are not true replicate simulations. If you
> want to prove repeatability, you need to repeat exactly what you did in
> the first case multiple times, with the only difference being either (1)
> a different initial configuration or (2) the same configuration with
> different initial velocities. The initial condition is what needs to
> change, and then you need to equilibrate and perform the simulation the
> same way to see if the same behavior arises.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From yepingsun80 at gmail.com  Fri Jan  3 02:25:20 2020
From: yepingsun80 at gmail.com (Sun Yeping)
Date: Fri, 03 Jan 2020 01:25:20 -0000
Subject: [gmx-users] What is the "gen-vel" used for?
In-Reply-To: <CAJOhvFmrhZfEGbiAq_7dhkgv5t_4-UR5rHuH=S_qgqL7r4z9fg@mail.gmail.com>
References: <6013cc34-2bd1-4dc3-912f-06d0f63e7c27.sunyeping@aliyun.com>
	<ec2fbb96-235f-98d9-ca6f-cb1bf81d75de@vt.edu>
	<852cf0ed-e2b1-4c59-8fc2-03955f8a60ab.sunyeping@aliyun.com>
	<91200d3b-d3d0-d909-dac1-33589f5ca1ae@vt.edu>
	<CAJOhvFmrhZfEGbiAq_7dhkgv5t_4-UR5rHuH=S_qgqL7r4z9fg@mail.gmail.com>
Message-ID: <CAJOhvFm2wF_MODoq_pJn64fo44PCpymPTNfP4AAR8ZdD=hm3YQ@mail.gmail.com>

Hello Justin,

Your reply is very helpful. I can understand the first method for proving
repeatablity: use a different initial configuration. But how to set the
different initial velocities with the same initial configuration if not
using the "gen-vel" option in the .mdp file for the production simulations?

Best regards,
Yeping

From jalemkul at vt.edu  Fri Jan  3 02:48:14 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Fri, 03 Jan 2020 01:48:14 -0000
Subject: [gmx-users] atom moved too far
In-Reply-To: <CAAHQ3wmpoDWc1BNT90XsEARLe9gV=AVCCejonzouFvOtXqefeA@mail.gmail.com>
References: <CAAHQ3wnYn0XapewAPd0RoAsC0HZLVJ_CjYU5bZOtDPd=u8aw4g@mail.gmail.com>
	<eb6b4386-8d1c-0a69-d59b-bde928a48d87@vt.edu>
	<CAAHQ3wmpoDWc1BNT90XsEARLe9gV=AVCCejonzouFvOtXqefeA@mail.gmail.com>
Message-ID: <edcb7673-b113-dcc4-810d-125ef89842f5@vt.edu>



On 1/2/20 3:02 PM, Christos Deligkaris wrote:
> thank you Justin.
>
> I saw on your umbrella sampling tutorial how to implement the restraints
> using the pull code.
>
> The protocol I used is (if I understand correctly your question): The
> energy minimization reached the cutoff for maximum force 1000 in 346 steps.
> My NVT equilibration was 50,000 steps of dt = 0.002 and I used 8 NPT
> equilibration calculations, each with 31,250 steps of dt=0.002 (total NPT
> equilibration time 500ps) where I slowly decreased the position restraints
> on DNA and the small molecule, as well as the harmonic restraint between
> the two.
> What are the best temperature coupling groups to use when we are not
> certain whether the small molecule will spend the entire simulation period
> physically bound to the macromolecule or whether it will become fully
> solvated at some point? Is Macromolecule and Non-macromolecule the best
> option since the small molecule will always (to a small or large extent)
> interact with water (versus the Macromolecule_and_small_molecule and
> everything else grouping option)?

I doubt there would be a measurable or provable difference between the 
behaviors of the two setups.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From jalemkul at vt.edu  Fri Jan  3 02:49:52 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Fri, 03 Jan 2020 01:49:52 -0000
Subject: [gmx-users] What is the "gen-vel" used for?
In-Reply-To: <CAJOhvFm2wF_MODoq_pJn64fo44PCpymPTNfP4AAR8ZdD=hm3YQ@mail.gmail.com>
References: <6013cc34-2bd1-4dc3-912f-06d0f63e7c27.sunyeping@aliyun.com>
	<ec2fbb96-235f-98d9-ca6f-cb1bf81d75de@vt.edu>
	<852cf0ed-e2b1-4c59-8fc2-03955f8a60ab.sunyeping@aliyun.com>
	<91200d3b-d3d0-d909-dac1-33589f5ca1ae@vt.edu>
	<CAJOhvFmrhZfEGbiAq_7dhkgv5t_4-UR5rHuH=S_qgqL7r4z9fg@mail.gmail.com>
	<CAJOhvFm2wF_MODoq_pJn64fo44PCpymPTNfP4AAR8ZdD=hm3YQ@mail.gmail.com>
Message-ID: <cd60d1ed-2c3e-a289-4536-ed2388d7960e@vt.edu>



On 1/2/20 8:25 PM, Sun Yeping wrote:
> Hello Justin,
>
> Your reply is very helpful. I can understand the first method for proving
> repeatablity: use a different initial configuration. But how to set the
> different initial velocities with the same initial configuration if not
> using the "gen-vel" option in the .mdp file for the production simulations?

Again, you don't generate velocities at the outset of a "production" 
simulation. You're creating a randomized system that needs to be 
re-equilibrated. Hence, velocities are only ever generated at the outset 
of the first step of equilibration. Perhaps this is just a discrepancy 
in terminology, but one cannot justifiably start a "production" 
simulation (i.e. one in which data are collected) from a totally random 
state that may not even be stable.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From yepingsun80 at gmail.com  Fri Jan  3 04:08:03 2020
From: yepingsun80 at gmail.com (Sun Yeping)
Date: Fri, 03 Jan 2020 03:08:03 -0000
Subject: [gmx-users] What is the "gen-vel" used for?
In-Reply-To: <cd60d1ed-2c3e-a289-4536-ed2388d7960e@vt.edu>
References: <6013cc34-2bd1-4dc3-912f-06d0f63e7c27.sunyeping@aliyun.com>
	<ec2fbb96-235f-98d9-ca6f-cb1bf81d75de@vt.edu>
	<852cf0ed-e2b1-4c59-8fc2-03955f8a60ab.sunyeping@aliyun.com>
	<91200d3b-d3d0-d909-dac1-33589f5ca1ae@vt.edu>
	<CAJOhvFmrhZfEGbiAq_7dhkgv5t_4-UR5rHuH=S_qgqL7r4z9fg@mail.gmail.com>
	<CAJOhvFm2wF_MODoq_pJn64fo44PCpymPTNfP4AAR8ZdD=hm3YQ@mail.gmail.com>
	<cd60d1ed-2c3e-a289-4536-ed2388d7960e@vt.edu>
Message-ID: <CAJOhvFmCfm1SqQtjuH1ev4D6ce-TmxjCZQku30xLP9HQBf4YUw@mail.gmail.com>

I guess I understand what you mean, but could you clarify it further? I
usually perform the simulations by the following process:

(1) energy minimization (EM); (2) NVT for 1 ns with heavy atom restraints;
(3) NPT for 1 ns with heavy atom restrains; (4) production simulation
without restraints.

To prove repeatability, I think I need to set up several parallel
simulations. Could I perform the NPT step for 3 different durations such as
1 ns, 2 ns, 5 ns to get three different velocities at the final frame of
the three NPT simulations, and remove the restraints and continue the
simulation from these velocities respectively? Thus I will get three
production simulations start from different velocities.

Or do I need to stop a so-called production simulations (without restraint)
at different time points and get three configurations, and repeat the EM,
NVT, NPT and production simulation steps for the three configurations
respectively to get three independent trajectories?

Best regards,

Yeping

On Fri, Jan 3, 2020 at 9:50 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/2/20 8:25 PM, Sun Yeping wrote:
> > Hello Justin,
> >
> > Your reply is very helpful. I can understand the first method for proving
> > repeatablity: use a different initial configuration. But how to set the
> > different initial velocities with the same initial configuration if not
> > using the "gen-vel" option in the .mdp file for the production
> simulations?
>
> Again, you don't generate velocities at the outset of a "production"
> simulation. You're creating a randomized system that needs to be
> re-equilibrated. Hence, velocities are only ever generated at the outset
> of the first step of equilibration. Perhaps this is just a discrepancy
> in terminology, but one cannot justifiably start a "production"
> simulation (i.e. one in which data are collected) from a totally random
> state that may not even be stable.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From dmaji43 at gmail.com  Fri Jan  3 06:11:02 2020
From: dmaji43 at gmail.com (Dhrubajyoti Maji)
Date: Fri, 03 Jan 2020 05:11:02 -0000
Subject: [gmx-users] nrexcl value for ions
Message-ID: <CACrPy4D8gKgu2c6KUzC_vSmrK3YKDyMkVLiFBZ093ngxCKgtKw@mail.gmail.com>

Dear gromacs users,
     A very happy new year to all of you. I an trying to simulate LiBr and
LiNO3. What will be the value of nrexcl in OPLS itp file for respective
cation and anions? I found nrexcl=1 for atomic ions in ions.itp file in
gromacs. Again in a tutorial of simulation of Choline Chloride + urea, they
have used nrecxl=3 for chloride ion. Here, I am confused about this. Any
kind of help will be highly appreciated.
Thanks and regards,
Dhrubajyoti Maji

From pragati2325 at gmail.com  Fri Jan  3 07:33:26 2020
From: pragati2325 at gmail.com (Pragati Sharma)
Date: Fri, 03 Jan 2020 06:33:26 -0000
Subject: [gmx-users] specific heat calculation using "gmx dos"
Message-ID: <CAMpF9Q1NQK_aMZK44qA6RDaOigvxHhfSkCnkyBcQ5GeLtHtRAA@mail.gmail.com>

 Dear all,

I am trying to calculate heat capacity of a polymeric system (30k atoms)
using gromacs.
I tried the classical way from the fluctuation dependent properties using
"gmx energy", but the values are not matching experimental values.

I want to use "gmx dos" program, but I have some confusions.

1. Does it gives only the quantum corrections in heat capacity, which
should be added to the one calculated from 'gmx energy' or  Does it gives
full heat capacity value including quantum corrections.

2. Should I have to run NVT simulations, run gmx dos, find Cv and the add
then calculate Cp, as given in the paper ( J. Chem. Theory Comput. 2012, 8,
61?74), *OR*
I can run a NPT simulation and calculate Cp from gmx dos.

3. gmx dos gives the Cp/Cv value in "dos.log" file. but is there any output
file to check its convergence. I mean how should I decide, how long the
trajectory I should take.

4. Cp can be calculated from the slope of enthalpy vs temp plot (dH/dT) (in
a small range of temp), what limitation does this approach have.

Thanks in advance.

From tdeepanshi248 at gmail.com  Fri Jan  3 12:01:24 2020
From: tdeepanshi248 at gmail.com (Deepanshi .)
Date: Fri, 03 Jan 2020 11:01:24 -0000
Subject: [gmx-users] compressibility values in coarse grained simulations
Message-ID: <CAB16xbSrgk718ge2r-v6=fjDzivN1cbOjHo9xiHXO=HZQtqgMg@mail.gmail.com>

Dear all,

I am using the coarse-grained molecular dynamics simulation to study
membranes. In the production run .mdp file, to control the pressure I am
using semiisotropic in the Pcoupltype option. I wanted to ask how many
values I should give to compressibility and ref_p and what will happen if I
give more or fewer values than the actual values?
Also, I wanted to ask that for coarse-grained simulations the value for
compressibility should be 3e-5 or 4e-5?

Thanks.

Regards,
Deepanshi.

From shradheyagupta at gmail.com  Fri Jan  3 12:53:31 2020
From: shradheyagupta at gmail.com (Shradheya R.R. Gupta)
Date: Fri, 03 Jan 2020 11:53:31 -0000
Subject: [gmx-users] Extending simulation
Message-ID: <CAGq6BhMHKrrG=sOKKuadSeKUh+Ehup6YWwirmi5i6KHJQi5mkg@mail.gmail.com>

Hello,
I have done simulation for 50 ns. After visualizing I came to the
conclusion that it need more simulation of 10 ns.
To do so I use :

gmx convert-tpr -s md_0_10.tpr -extend 10000 -o md_0_60.tpr

It showed:
Reading toplogy and stuff from md_0_10.tpr
Reading file md_0_10.tpr, VERSION 2019 (single precision)
Extending remaining runtime of by 10000 ps (now 30000000 steps)
Writing statusfile with starting step          0 and length   30000000 steps...
                                 time      0.000 and length  60000.000 ps

Then I used:
gmx mdrun -s  md_0_60.tpr -cpi md_0_10.cpt -deffnm md_0_10

The simulation started for 60 ns instead of which I want it start from the 50 ns

how to do this

thanks

From shradheyagupta at gmail.com  Fri Jan  3 12:54:12 2020
From: shradheyagupta at gmail.com (Shradheya R.R. Gupta)
Date: Fri, 03 Jan 2020 11:54:12 -0000
Subject: [gmx-users] Extending simulation
Message-ID: <CAGq6BhMHKrrG=sOKKuadSeKUh+Ehup6YWwirmi5i6KHJQi5mkg@mail.gmail.com>

Hello,
I have done simulation for 50 ns. After visualizing I came to the
conclusion that it need more simulation of 10 ns.
To do so I use :

gmx convert-tpr -s md_0_10.tpr -extend 10000 -o md_0_60.tpr

It showed:
Reading toplogy and stuff from md_0_10.tpr
Reading file md_0_10.tpr, VERSION 2019 (single precision)
Extending remaining runtime of by 10000 ps (now 30000000 steps)
Writing statusfile with starting step          0 and length   30000000 steps...
                                 time      0.000 and length  60000.000 ps

Then I used:
gmx mdrun -s  md_0_60.tpr -cpi md_0_10.cpt -deffnm md_0_10

The simulation started for 60 ns instead of which I want it start from the 50 ns

how to do this

thanks

From naveenbk4717 at gmail.com  Fri Jan  3 13:50:07 2020
From: naveenbk4717 at gmail.com (Naveen BK)
Date: Fri, 03 Jan 2020 12:50:07 -0000
Subject: [gmx-users] Extending simulation
In-Reply-To: <CAGq6BhMHKrrG=sOKKuadSeKUh+Ehup6YWwirmi5i6KHJQi5mkg@mail.gmail.com>
References: <CAGq6BhMHKrrG=sOKKuadSeKUh+Ehup6YWwirmi5i6KHJQi5mkg@mail.gmail.com>
Message-ID: <CANznyrsS4TZbUrKa1R-fk=wJOyfwn5=jQUPwMWwJ+-sTT2-vgQ@mail.gmail.com>

gmx mdrun -s  md_0_60.tpr   -cpi  md_0_10.cpt   -noappend

this command will start from previous step.
Thanks and Regards,
Naveen BK,
MSc in bioinformatics,
+918123474717.


On Fri, Jan 3, 2020 at 5:23 PM Shradheya R.R. Gupta <
shradheyagupta at gmail.com> wrote:

> Hello,
> I have done simulation for 50 ns. After visualizing I came to the
> conclusion that it need more simulation of 10 ns.
> To do so I use :
>
> gmx convert-tpr -s md_0_10.tpr -extend 10000 -o md_0_60.tpr
>
> It showed:
> Reading toplogy and stuff from md_0_10.tpr
> Reading file md_0_10.tpr, VERSION 2019 (single precision)
> Extending remaining runtime of by 10000 ps (now 30000000 steps)
> Writing statusfile with starting step          0 and length   30000000
> steps...
>                                  time      0.000 and length  60000.000 ps
>
> Then I used:
> gmx mdrun -s  md_0_60.tpr -cpi md_0_10.cpt -deffnm md_0_10
>
> The simulation started for 60 ns instead of which I want it start from the
> 50 ns
>
> how to do this
>
> thanks
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From naveenbk4717 at gmail.com  Fri Jan  3 13:50:07 2020
From: naveenbk4717 at gmail.com (Naveen BK)
Date: Fri, 03 Jan 2020 12:50:07 -0000
Subject: [gmx-users] Extending simulation
In-Reply-To: <CAGq6BhMHKrrG=sOKKuadSeKUh+Ehup6YWwirmi5i6KHJQi5mkg@mail.gmail.com>
References: <CAGq6BhMHKrrG=sOKKuadSeKUh+Ehup6YWwirmi5i6KHJQi5mkg@mail.gmail.com>
Message-ID: <CANznyrsS4TZbUrKa1R-fk=wJOyfwn5=jQUPwMWwJ+-sTT2-vgQ@mail.gmail.com>

gmx mdrun -s  md_0_60.tpr   -cpi  md_0_10.cpt   -noappend

this command will start from previous step.
Thanks and Regards,
Naveen BK,
MSc in bioinformatics,
+918123474717.


On Fri, Jan 3, 2020 at 5:23 PM Shradheya R.R. Gupta <
shradheyagupta at gmail.com> wrote:

> Hello,
> I have done simulation for 50 ns. After visualizing I came to the
> conclusion that it need more simulation of 10 ns.
> To do so I use :
>
> gmx convert-tpr -s md_0_10.tpr -extend 10000 -o md_0_60.tpr
>
> It showed:
> Reading toplogy and stuff from md_0_10.tpr
> Reading file md_0_10.tpr, VERSION 2019 (single precision)
> Extending remaining runtime of by 10000 ps (now 30000000 steps)
> Writing statusfile with starting step          0 and length   30000000
> steps...
>                                  time      0.000 and length  60000.000 ps
>
> Then I used:
> gmx mdrun -s  md_0_60.tpr -cpi md_0_10.cpt -deffnm md_0_10
>
> The simulation started for 60 ns instead of which I want it start from the
> 50 ns
>
> how to do this
>
> thanks
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From pradeepakumari94 at gmail.com  Fri Jan  3 15:16:22 2020
From: pradeepakumari94 at gmail.com (Pradeepa Kumari)
Date: Fri, 03 Jan 2020 14:16:22 -0000
Subject: [gmx-users] Atomic/residue fluctuations in z direction
Message-ID: <CAG32QRV2LY6MK6ft_Z1iDPYQgmhrB9xzNHShYHQT-v9sn5xR0g@mail.gmail.com>

Can we obtain atomic fluctuations in z direction using gromacs rmsf tool ?
or Is there any other tool for this purpose

Thanking you in advance.

Regards,
dananjana

From navneetcdl at gmail.com  Fri Jan  3 18:47:08 2020
From: navneetcdl at gmail.com (Navneet Kumar)
Date: Fri, 03 Jan 2020 17:47:08 -0000
Subject: [gmx-users] Position restrain and other error while doing simulation
Message-ID: <CAOvdM4WNVA27VUacpYFoqpn_s8vvZnZSqZPW1kL1D59GU0wcNA@mail.gmail.com>

Hello Everyone!


I am trying to simulate a system having a small protein and 10 small
molecules randomly distributed in box. I prepared the system using the
PACKMOL.

I am using the GROMACS 2018.4 and using "GROMOS96 54a7 force field.
Prepared the ligand topology ATB server.
Everything went fine till the addition of counter ions to neutralize the
system.
Aim of simulation is to study the interaction of protein and ligand.

Since small molecules are randomly distributed in box do I need to do these
steps
-Applying restrain to ligands
-Treatment of temperature coupling groups.

How to deal with this error.

Command line:
  gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr

Ignoring obsolete mdp entry 'title'
Setting the LD random seed to -685300895
Generated 210 of the 2556 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_chain_C'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'OMSD'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'NA'
turning all bonds into constraints...
Setting gen_seed to -369358517
Velocities were taken from a Maxwell distribution at 310 K
Removing all charge groups because cutoff-scheme=Verlet

-------------------------------------------------------
Program:     gmx grompp, version 2018.4
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2008)

Fatal error:
Cannot find position restraint file restraint.gro (option -r).
>From GROMACS-2018, you need to specify the position restraint coordinate
files
explicitly to avoid mistakes, although you can still use the same file as
you
specify for the -c option.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------






-- 






     Thanks & Regards
_______________________________________________________

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneetcdl at gmail.com  <navneetcdl at gmail.com>
<http://www.linkedin.com/in/navneet-kumar-74391814a/>
<http://facebook.com/xeon.singh> <http://instagram.com/snavneetkumar>

Please consider your environmental responsibility. Before printing this
e-mail message, ask yourself whether you really need a hard copy.

From nchaudha at andrew.cmu.edu  Fri Jan  3 19:13:06 2020
From: nchaudha at andrew.cmu.edu (Namit Chaudhary)
Date: Fri, 03 Jan 2020 18:13:06 -0000
Subject: [gmx-users] Bilayer exploding with semiisotropic coupling
Message-ID: <CANTDrdHmTKV1VOoW9=2A2z8U4_BLbdtVgLaCo0SU6iH=RYCftQ@mail.gmail.com>

Hi all,

I am trying to simulate a coarse grain system containing DPPC (10%),
Cholesterol (40%) and a custom lipid that's synthesized by our lab (50%,
topology and martini mapping attached).  Our lab uses these molecules to
formulate lipid nanoparticles and deliver RNA therapeutics. I am trying to
understand the structure of these nanoparticles. I tried modelling them as
a bilayer but the system seems to be exploding in the z - direction during
the production run if I use semiisotropic or anisotropic pressure coupling
(isotropic coupling seems to work).  Below is the md.mdp file that I am
using.

integrator               = md
dt                           = 0.01
nsteps                   = 8000000
nstcomm               = 100
comm-grps            = LIPIDS SOL


nstxout                  = 0
nstvout                  = 0
nstfout                  = 0
nstlog                   = 1000  ; Output frequency for energies to log
file
nstenergy                = 100   ; Output frequency for energies to energy
file
nstxtcout                = 1000  ; Output frequency for .xtc file
xtc_precision            = 100
xtc-grps                 =
energygrps               =


nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.1

coulombtype              = reaction_field  ;Reaction_field (for use with
Verlet-pairlist) ;PME (especially with polarizable water)
rcoulomb_switch          = 0.0
rcoulomb                 = 1.1
epsilon_r                = 15 ; 2.5 (with polarizable water)
vdw_type                 = cutoff  ;cutoff (for use with Verlet-pairlist)
rvdw_switch              = 0.9
rvdw                     = 1.1 ;1.1 (for use with Verlet-pairlist)

cutoff-scheme            = verlet

tcoupl                   = v-rescale
tc-grps                  = LIPIDS SOL
tau_t                     = 1.0  1.0
ref_t                      = 298 298
Pcoupl                   = parrinello-rahman
Pcoupltype            = semiisotropic
tau_p                     = 12.0
compressibility       = 3e-4 3e-4      ; 3e-4
ref_p                      = 1.0 1.0       ; 1.0 1.0

gen_vel                    = yes
gen_temp                 = 298
gen_seed                 = 473529

constraints                = none
constraint_algorithm = Lincs
continuation              = no
lincs_order                = 4
lincs_warnangle        = 30

Is there something that I can change in my mdp file? Or is there something
wrong with the lipid itself?


Thank you
Namit

From nchaudha at andrew.cmu.edu  Fri Jan  3 19:29:36 2020
From: nchaudha at andrew.cmu.edu (Namit Chaudhary)
Date: Fri, 03 Jan 2020 18:29:36 -0000
Subject: [gmx-users] Bilayer exploding with semiisotropic coupling
In-Reply-To: <CANTDrdHmTKV1VOoW9=2A2z8U4_BLbdtVgLaCo0SU6iH=RYCftQ@mail.gmail.com>
References: <CANTDrdHmTKV1VOoW9=2A2z8U4_BLbdtVgLaCo0SU6iH=RYCftQ@mail.gmail.com>
Message-ID: <CANTDrdHUxxgzCnF=_vFeELn3cfBoZYfEY4QOXHprt_UyHs5Eyw@mail.gmail.com>

Hi,

Sorry. I didn't realize that attachments aren't uploaded. Below is a link
for the files mentioned in the original mail.
https://drive.google.com/drive/folders/1fUrx4yt3DpCEGY0CACA6n-PXcswfaa31?usp=sharing

Namit

On Fri, Jan 3, 2020 at 1:12 PM Namit Chaudhary <nchaudha at andrew.cmu.edu>
wrote:

> Hi all,
>
> I am trying to simulate a coarse grain system containing DPPC (10%),
> Cholesterol (40%) and a custom lipid that's synthesized by our lab (50%,
> topology and martini mapping attached).  Our lab uses these molecules to
> formulate lipid nanoparticles and deliver RNA therapeutics. I am trying to
> understand the structure of these nanoparticles. I tried modelling them as
> a bilayer but the system seems to be exploding in the z - direction during
> the production run if I use semiisotropic or anisotropic pressure coupling
> (isotropic coupling seems to work).  Below is the md.mdp file that I am
> using.
>
> integrator               = md
> dt                           = 0.01
> nsteps                   = 8000000
> nstcomm               = 100
> comm-grps            = LIPIDS SOL
>
>
> nstxout                  = 0
> nstvout                  = 0
> nstfout                  = 0
> nstlog                   = 1000  ; Output frequency for energies to log
> file
> nstenergy                = 100   ; Output frequency for energies to energy
> file
> nstxtcout                = 1000  ; Output frequency for .xtc file
> xtc_precision            = 100
> xtc-grps                 =
> energygrps               =
>
>
> nstlist                  = 10
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 1.1
>
> coulombtype              = reaction_field  ;Reaction_field (for use with
> Verlet-pairlist) ;PME (especially with polarizable water)
> rcoulomb_switch          = 0.0
> rcoulomb                 = 1.1
> epsilon_r                = 15 ; 2.5 (with polarizable water)
> vdw_type                 = cutoff  ;cutoff (for use with Verlet-pairlist)
>
> rvdw_switch              = 0.9
> rvdw                     = 1.1 ;1.1 (for use with Verlet-pairlist)
>
> cutoff-scheme            = verlet
>
> tcoupl                   = v-rescale
> tc-grps                  = LIPIDS SOL
> tau_t                     = 1.0  1.0
> ref_t                      = 298 298
> Pcoupl                   = parrinello-rahman
> Pcoupltype            = semiisotropic
> tau_p                     = 12.0
> compressibility       = 3e-4 3e-4      ; 3e-4
> ref_p                      = 1.0 1.0       ; 1.0 1.0
>
> gen_vel                    = yes
> gen_temp                 = 298
> gen_seed                 = 473529
>
> constraints                = none
> constraint_algorithm = Lincs
> continuation              = no
> lincs_order                = 4
> lincs_warnangle        = 30
>
> Is there something that I can change in my mdp file? Or is there something
> wrong with the lipid itself?
>
>
> Thank you
> Namit
>


-- 
*Namit Chaudhary*
Chemical Engineering | Carnegie Mellon University
M: 724-506-0693 | E: nchaudha at andrew.cmu.edu

From vuqv.phys at gmail.com  Fri Jan  3 20:02:29 2020
From: vuqv.phys at gmail.com (Quyen V. Vu)
Date: Fri, 03 Jan 2020 19:02:29 -0000
Subject: [gmx-users] Position restrain and other error while doing
	simulation
In-Reply-To: <CAOvdM4WNVA27VUacpYFoqpn_s8vvZnZSqZPW1kL1D59GU0wcNA@mail.gmail.com>
References: <CAOvdM4WNVA27VUacpYFoqpn_s8vvZnZSqZPW1kL1D59GU0wcNA@mail.gmail.com>
Message-ID: <CA+CKAfzABn-jxXm0oZgE30hG++dXjna3XuQ=+foak3Wmqs-Ghw@mail.gmail.com>

It's obvious from the error that you did not specify the position restraint
coordinates file while the define directive in mdp says using restraint.
As grompp suggestion:   gmx grompp -f nvt.mdp -c em.gro *-r em.gro* -p
topol.top -o nvt.tpr


On Fri, Jan 3, 2020 at 6:47 PM Navneet Kumar <navneetcdl at gmail.com> wrote:

> Hello Everyone!
>
>
> I am trying to simulate a system having a small protein and 10 small
> molecules randomly distributed in box. I prepared the system using the
> PACKMOL.
>
> I am using the GROMACS 2018.4 and using "GROMOS96 54a7 force field.
> Prepared the ligand topology ATB server.
> Everything went fine till the addition of counter ions to neutralize the
> system.
> Aim of simulation is to study the interaction of protein and ligand.
>
> Since small molecules are randomly distributed in box do I need to do these
> steps
> -Applying restrain to ligands
> -Treatment of temperature coupling groups.
>
> How to deal with this error.
>
> Command line:
>   gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr
>
> Ignoring obsolete mdp entry 'title'
> Setting the LD random seed to -685300895
> Generated 210 of the 2556 non-bonded parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'Protein_chain_C'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'OMSD'
> turning all bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning all bonds into constraints...
> Excluding 1 bonded neighbours molecule type 'NA'
> turning all bonds into constraints...
> Setting gen_seed to -369358517
> Velocities were taken from a Maxwell distribution at 310 K
> Removing all charge groups because cutoff-scheme=Verlet
>
> -------------------------------------------------------
> Program:     gmx grompp, version 2018.4
> Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2008)
>
> Fatal error:
> Cannot find position restraint file restraint.gro (option -r).
> From GROMACS-2018, you need to specify the position restraint coordinate
> files
> explicitly to avoid mistakes, although you can still use the same file as
> you
> specify for the -c option.
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
>
>
>
>
>
> --
>
>
>
>
>
>
>      Thanks & Regards
> _______________________________________________________
>
> [image: photo]
> *NAVNEET KUMAR*
> Doctoral Student
> Dept. of Pharmacoinformatics
> National Institute of Pharmaceutical Education and Research, Sector 67,
> S.A.S. Nagar - 160062, Punjab (INDIA)
> P +918017967647  <+918017967647> |
> E navneetcdl at gmail.com  <navneetcdl at gmail.com>
> <http://www.linkedin.com/in/navneet-kumar-74391814a/>
> <http://facebook.com/xeon.singh> <http://instagram.com/snavneetkumar>
>
> Please consider your environmental responsibility. Before printing this
> e-mail message, ask yourself whether you really need a hard copy.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From vuqv.phys at gmail.com  Fri Jan  3 20:03:18 2020
From: vuqv.phys at gmail.com (Quyen V. Vu)
Date: Fri, 03 Jan 2020 19:03:18 -0000
Subject: [gmx-users] Position restrain and other error while doing
	simulation
In-Reply-To: <CAOvdM4WNVA27VUacpYFoqpn_s8vvZnZSqZPW1kL1D59GU0wcNA@mail.gmail.com>
References: <CAOvdM4WNVA27VUacpYFoqpn_s8vvZnZSqZPW1kL1D59GU0wcNA@mail.gmail.com>
Message-ID: <CA+CKAfzABn-jxXm0oZgE30hG++dXjna3XuQ=+foak3Wmqs-Ghw@mail.gmail.com>

It's obvious from the error that you did not specify the position restraint
coordinates file while the define directive in mdp says using restraint.
As grompp suggestion:   gmx grompp -f nvt.mdp -c em.gro *-r em.gro* -p
topol.top -o nvt.tpr


On Fri, Jan 3, 2020 at 6:47 PM Navneet Kumar <navneetcdl at gmail.com> wrote:

> Hello Everyone!
>
>
> I am trying to simulate a system having a small protein and 10 small
> molecules randomly distributed in box. I prepared the system using the
> PACKMOL.
>
> I am using the GROMACS 2018.4 and using "GROMOS96 54a7 force field.
> Prepared the ligand topology ATB server.
> Everything went fine till the addition of counter ions to neutralize the
> system.
> Aim of simulation is to study the interaction of protein and ligand.
>
> Since small molecules are randomly distributed in box do I need to do these
> steps
> -Applying restrain to ligands
> -Treatment of temperature coupling groups.
>
> How to deal with this error.
>
> Command line:
>   gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr
>
> Ignoring obsolete mdp entry 'title'
> Setting the LD random seed to -685300895
> Generated 210 of the 2556 non-bonded parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'Protein_chain_C'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'OMSD'
> turning all bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning all bonds into constraints...
> Excluding 1 bonded neighbours molecule type 'NA'
> turning all bonds into constraints...
> Setting gen_seed to -369358517
> Velocities were taken from a Maxwell distribution at 310 K
> Removing all charge groups because cutoff-scheme=Verlet
>
> -------------------------------------------------------
> Program:     gmx grompp, version 2018.4
> Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2008)
>
> Fatal error:
> Cannot find position restraint file restraint.gro (option -r).
> From GROMACS-2018, you need to specify the position restraint coordinate
> files
> explicitly to avoid mistakes, although you can still use the same file as
> you
> specify for the -c option.
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
>
>
>
>
>
> --
>
>
>
>
>
>
>      Thanks & Regards
> _______________________________________________________
>
> [image: photo]
> *NAVNEET KUMAR*
> Doctoral Student
> Dept. of Pharmacoinformatics
> National Institute of Pharmaceutical Education and Research, Sector 67,
> S.A.S. Nagar - 160062, Punjab (INDIA)
> P +918017967647  <+918017967647> |
> E navneetcdl at gmail.com  <navneetcdl at gmail.com>
> <http://www.linkedin.com/in/navneet-kumar-74391814a/>
> <http://facebook.com/xeon.singh> <http://instagram.com/snavneetkumar>
>
> Please consider your environmental responsibility. Before printing this
> e-mail message, ask yourself whether you really need a hard copy.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From navneetcdl at gmail.com  Fri Jan  3 20:10:57 2020
From: navneetcdl at gmail.com (Navneet Kumar)
Date: Fri, 03 Jan 2020 19:10:57 -0000
Subject: [gmx-users] Position restrain and other error while doing
	simulation
In-Reply-To: <CA+CKAfzABn-jxXm0oZgE30hG++dXjna3XuQ=+foak3Wmqs-Ghw@mail.gmail.com>
References: <CAOvdM4WNVA27VUacpYFoqpn_s8vvZnZSqZPW1kL1D59GU0wcNA@mail.gmail.com>
	<CA+CKAfzABn-jxXm0oZgE30hG++dXjna3XuQ=+foak3Wmqs-Ghw@mail.gmail.com>
Message-ID: <CAOvdM4WRjGXNMHUTV6VNwfku675k1pm_Jm-X8V3Rgsu=Eo9N7A@mail.gmail.com>

Do I need to  Applying restrain to ligands
-Treatment of temperature coupling groups as we do in protein ligand
complex bound to each other. But in my case ligands are randomly
distributed around protein. What should a mdp file look like in this case.
I am trying to simulate the beta amyloid with some Polyphenols to see
effect of these molecules on beta amyloid aggregation.

On Sat, 4 Jan 2020, 00:33 Quyen V. Vu, <vuqv.phys at gmail.com> wrote:

> It's obvious from the error that you did not specify the position restraint
> coordinates file while the define directive in mdp says using restraint.
> As grompp suggestion:   gmx grompp -f nvt.mdp -c em.gro *-r em.gro* -p
> topol.top -o nvt.tpr
>
>
> On Fri, Jan 3, 2020 at 6:47 PM Navneet Kumar <navneetcdl at gmail.com> wrote:
>
> > Hello Everyone!
> >
> >
> > I am trying to simulate a system having a small protein and 10 small
> > molecules randomly distributed in box. I prepared the system using the
> > PACKMOL.
> >
> > I am using the GROMACS 2018.4 and using "GROMOS96 54a7 force field.
> > Prepared the ligand topology ATB server.
> > Everything went fine till the addition of counter ions to neutralize the
> > system.
> > Aim of simulation is to study the interaction of protein and ligand.
> >
> > Since small molecules are randomly distributed in box do I need to do
> these
> > steps
> > -Applying restrain to ligands
> > -Treatment of temperature coupling groups.
> >
> > How to deal with this error.
> >
> > Command line:
> >   gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr
> >
> > Ignoring obsolete mdp entry 'title'
> > Setting the LD random seed to -685300895
> > Generated 210 of the 2556 non-bonded parameter combinations
> > Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
> > turning all bonds into constraints...
> > Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
> > turning all bonds into constraints...
> > Excluding 3 bonded neighbours molecule type 'Protein_chain_C'
> > turning all bonds into constraints...
> > Excluding 3 bonded neighbours molecule type 'OMSD'
> > turning all bonds into constraints...
> > Excluding 2 bonded neighbours molecule type 'SOL'
> > turning all bonds into constraints...
> > Excluding 1 bonded neighbours molecule type 'NA'
> > turning all bonds into constraints...
> > Setting gen_seed to -369358517
> > Velocities were taken from a Maxwell distribution at 310 K
> > Removing all charge groups because cutoff-scheme=Verlet
> >
> > -------------------------------------------------------
> > Program:     gmx grompp, version 2018.4
> > Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2008)
> >
> > Fatal error:
> > Cannot find position restraint file restraint.gro (option -r).
> > From GROMACS-2018, you need to specify the position restraint coordinate
> > files
> > explicitly to avoid mistakes, although you can still use the same file as
> > you
> > specify for the -c option.
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > -------------------------------------------------------
> >
> >
> >
> >
> >
> >
> > --
> >
> >
> >
> >
> >
> >
> >      Thanks & Regards
> > _______________________________________________________
> >
> > [image: photo]
> > *NAVNEET KUMAR*
> > Doctoral Student
> > Dept. of Pharmacoinformatics
> > National Institute of Pharmaceutical Education and Research, Sector 67,
> > S.A.S. Nagar - 160062, Punjab (INDIA)
> > P +918017967647  <+918017967647> |
> > E navneetcdl at gmail.com  <navneetcdl at gmail.com>
> > <http://www.linkedin.com/in/navneet-kumar-74391814a/>
> > <http://facebook.com/xeon.singh> <http://instagram.com/snavneetkumar>
> >
> > Please consider your environmental responsibility. Before printing this
> > e-mail message, ask yourself whether you really need a hard copy.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From jalemkul at vt.edu  Fri Jan  3 20:29:23 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Fri, 03 Jan 2020 19:29:23 -0000
Subject: [gmx-users] What is the "gen-vel" used for?
In-Reply-To: <CAJOhvFmCfm1SqQtjuH1ev4D6ce-TmxjCZQku30xLP9HQBf4YUw@mail.gmail.com>
References: <6013cc34-2bd1-4dc3-912f-06d0f63e7c27.sunyeping@aliyun.com>
	<ec2fbb96-235f-98d9-ca6f-cb1bf81d75de@vt.edu>
	<852cf0ed-e2b1-4c59-8fc2-03955f8a60ab.sunyeping@aliyun.com>
	<91200d3b-d3d0-d909-dac1-33589f5ca1ae@vt.edu>
	<CAJOhvFmrhZfEGbiAq_7dhkgv5t_4-UR5rHuH=S_qgqL7r4z9fg@mail.gmail.com>
	<CAJOhvFm2wF_MODoq_pJn64fo44PCpymPTNfP4AAR8ZdD=hm3YQ@mail.gmail.com>
	<cd60d1ed-2c3e-a289-4536-ed2388d7960e@vt.edu>
	<CAJOhvFmCfm1SqQtjuH1ev4D6ce-TmxjCZQku30xLP9HQBf4YUw@mail.gmail.com>
Message-ID: <54bed6d0-dd59-50b3-1a65-d44a803c7380@vt.edu>



On 1/2/20 10:07 PM, Sun Yeping wrote:
> I guess I understand what you mean, but could you clarify it further? I
> usually perform the simulations by the following process:
>
> (1) energy minimization (EM); (2) NVT for 1 ns with heavy atom restraints;
> (3) NPT for 1 ns with heavy atom restrains; (4) production simulation
> without restraints.
>
> To prove repeatability, I think I need to set up several parallel
> simulations. Could I perform the NPT step for 3 different durations such as
> 1 ns, 2 ns, 5 ns to get three different velocities at the final frame of
> the three NPT simulations, and remove the restraints and continue the
> simulation from these velocities respectively? Thus I will get three
> production simulations start from different velocities.
>
> Or do I need to stop a so-called production simulations (without restraint)
> at different time points and get three configurations, and repeat the EM,
> NVT, NPT and production simulation steps for the three configurations
> respectively to get three independent trajectories?

The conventional approach is to generate velocities at the beginning of 
what you have defined as step (2) above. Continuing NPT is basically 
just taking time points of the same run and continuing it. One could 
argue that those simulations will eventually diverge, but I don't think 
you can truly call them independent runs. They all started from the 
exact same input/state but were just allowed to run for different 
amounts of time.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From jalemkul at vt.edu  Fri Jan  3 20:30:48 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Fri, 03 Jan 2020 19:30:48 -0000
Subject: [gmx-users] nrexcl value for ions
In-Reply-To: <CACrPy4D8gKgu2c6KUzC_vSmrK3YKDyMkVLiFBZ093ngxCKgtKw@mail.gmail.com>
References: <CACrPy4D8gKgu2c6KUzC_vSmrK3YKDyMkVLiFBZ093ngxCKgtKw@mail.gmail.com>
Message-ID: <71a06e6a-9cf6-b723-ffdf-8e87654291a7@vt.edu>



On 1/3/20 12:10 AM, Dhrubajyoti Maji wrote:
> Dear gromacs users,
>       A very happy new year to all of you. I an trying to simulate LiBr and
> LiNO3. What will be the value of nrexcl in OPLS itp file for respective
> cation and anions? I found nrexcl=1 for atomic ions in ions.itp file in
> gromacs. Again in a tutorial of simulation of Choline Chloride + urea, they
> have used nrecxl=3 for chloride ion. Here, I am confused about this. Any
> kind of help will be highly appreciated.

There are no covalent bonds in monoatomic ions, so any value of nrexcl 
can be used. NO3 has a maximum of two contiguous covalent bonds so 
nrexcl = 2. Or you can set nrexcl = 3 for everything, which has the 
exact same effect.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From jalemkul at vt.edu  Fri Jan  3 20:31:23 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Fri, 03 Jan 2020 19:31:23 -0000
Subject: [gmx-users] Atomic/residue fluctuations in z direction
In-Reply-To: <CAG32QRV2LY6MK6ft_Z1iDPYQgmhrB9xzNHShYHQT-v9sn5xR0g@mail.gmail.com>
References: <CAG32QRV2LY6MK6ft_Z1iDPYQgmhrB9xzNHShYHQT-v9sn5xR0g@mail.gmail.com>
Message-ID: <d2f2858c-01bf-52a3-b7ec-2ad797fdc409@vt.edu>



On 1/3/20 9:16 AM, Pradeepa Kumari wrote:
> Can we obtain atomic fluctuations in z direction using gromacs rmsf tool ?
> or Is there any other tool for this purpose

Extract the z-coordinate time series with gmx traj -ox -z and compute 
fluctuations or whatever statistics you like.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From snehasis.chatterjee18 at gmail.com  Fri Jan  3 21:30:02 2020
From: snehasis.chatterjee18 at gmail.com (Snehasis Chatterjee)
Date: Fri, 03 Jan 2020 20:30:02 -0000
Subject: [gmx-users] query regarding center of mass removal
Message-ID: <CAEScH66GPJ2cmUJPTAh0m2U=nhCmaG4HmTisXiR_sfv11Zr0=w@mail.gmail.com>

Dear Gromacs users,

I am trying to perform a virus capsid simulation using GROMACS 2018. 240
Calcium ions bound to specific regions of the capsid and have important
role in maintaining capsid stability. In this context, I had a query
regarding the correct Center-of-Mass removal settings. I usually run
protein simulation in aqueous environment using following mdp options:



*nstcomm= 100comm_mode= linearcomm_grps= Protein Non-Protein*

In aqueous environment, I typically use "Protein Non-Protein," with
Non-Protein containing solvent and ions. Since, 240 Ca2+ ions are
non-covalently attached with the capsid, I am planing to couple  capsid
with Ca2+ ions. I am bit confused regarding this issue. Any kind of advice/
suggestions will be deeply appreciated.

Thanks in advance,
Snehasis Chatterjee

From jalemkul at vt.edu  Fri Jan  3 23:22:14 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Fri, 03 Jan 2020 22:22:14 -0000
Subject: [gmx-users] query regarding center of mass removal
In-Reply-To: <CAEScH66GPJ2cmUJPTAh0m2U=nhCmaG4HmTisXiR_sfv11Zr0=w@mail.gmail.com>
References: <CAEScH66GPJ2cmUJPTAh0m2U=nhCmaG4HmTisXiR_sfv11Zr0=w@mail.gmail.com>
Message-ID: <0087bf32-f571-8dc4-0fc5-2e73c65af126@vt.edu>



On 1/3/20 3:29 PM, Snehasis Chatterjee wrote:
> Dear Gromacs users,
>
> I am trying to perform a virus capsid simulation using GROMACS 2018. 240
> Calcium ions bound to specific regions of the capsid and have important
> role in maintaining capsid stability. In this context, I had a query
> regarding the correct Center-of-Mass removal settings. I usually run
> protein simulation in aqueous environment using following mdp options:
>
>
>
> *nstcomm= 100comm_mode= linearcomm_grps= Protein Non-Protein*
>
> In aqueous environment, I typically use "Protein Non-Protein," with
> Non-Protein containing solvent and ions. Since, 240 Ca2+ ions are
> non-covalently attached with the capsid, I am planing to couple  capsid
> with Ca2+ ions. I am bit confused regarding this issue. Any kind of advice/
> suggestions will be deeply appreciated.

For any system in an isotropic medium (i.e. water), comm-grps should be 
set to "system" because there are not multiple phases that may diffuse 
differently. You shouldn't use Protein/Non-Protein here; that's for tc-grps.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From neena.susaneappen at mail.utoronto.ca  Sat Jan  4 03:11:25 2020
From: neena.susaneappen at mail.utoronto.ca (Neena Susan Eappen)
Date: Sat, 04 Jan 2020 02:11:25 -0000
Subject: [gmx-users] What is the "gen-vel" used for?
Message-ID: <YT1PR01MB37234D43C1489F79C11FAEADCD220@YT1PR01MB3723.CANPRD01.PROD.OUTLOOK.COM>

Yeping Sun,

Quoting Justin's answer for a similar question I had on how to repeat a simulation say 10 times
 " To run 10 independent simulations, I would run minimization once and start from 10 new equilibration runs, each with a different set of initial velocities (change gen_seed or simply set to -1).That approach may not be as robust as starting from 10 different configurations, but the exact approach depends on the system in question".





From neena.susaneappen at mail.utoronto.ca  Sat Jan  4 03:36:42 2020
From: neena.susaneappen at mail.utoronto.ca (Neena Susan Eappen)
Date: Sat, 04 Jan 2020 02:36:42 -0000
Subject: [gmx-users] amide-capped C-terminus; OPLS force field
In-Reply-To: <YT1PR01MB37235801EA9515B3408021F0CD220@YT1PR01MB3723.CANPRD01.PROD.OUTLOOK.COM>
References: <mailman.426.1578079884.1966.gromacs.org_gmx-users@maillist.sys.kth.se>,
	<YT1PR01MB37239EF3CF2C4FE4256C1D3DCD220@YT1PR01MB3723.CANPRD01.PROD.OUTLOOK.COM>,
	<YT1PR01MB37235801EA9515B3408021F0CD220@YT1PR01MB3723.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <YT1PR01MB3723BF41D44ED7648364E666CD220@YT1PR01MB3723.CANPRD01.PROD.OUTLOOK.COM>

I do this by adding amide group at the C-terminus on Pymol, use -ter flag during gmx pdb2gmx command, select None (for C-terminus), N and H in that amide group are automatically recognized as atom types opls 237 and opls 240 respectively. The net charge of system remains neutral.

From dmaji43 at gmail.com  Sat Jan  4 06:01:35 2020
From: dmaji43 at gmail.com (Dhrubajyoti Maji)
Date: Sat, 04 Jan 2020 05:01:35 -0000
Subject: [gmx-users] nrexcl value for ions
In-Reply-To: <71a06e6a-9cf6-b723-ffdf-8e87654291a7@vt.edu>
References: <CACrPy4D8gKgu2c6KUzC_vSmrK3YKDyMkVLiFBZ093ngxCKgtKw@mail.gmail.com>
	<71a06e6a-9cf6-b723-ffdf-8e87654291a7@vt.edu>
Message-ID: <CACrPy4BsEr0AK9Nt-Tb=h8-feY+4DyypaS-TgRqg_ZBsK6fO5g@mail.gmail.com>

Thank you Prof. Lemkul for your kind reply.

Dhrubajyoti

On Sat, 4 Jan 2020 at 01:01, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/3/20 12:10 AM, Dhrubajyoti Maji wrote:
> > Dear gromacs users,
> >       A very happy new year to all of you. I an trying to simulate LiBr
> and
> > LiNO3. What will be the value of nrexcl in OPLS itp file for respective
> > cation and anions? I found nrexcl=1 for atomic ions in ions.itp file in
> > gromacs. Again in a tutorial of simulation of Choline Chloride + urea,
> they
> > have used nrecxl=3 for chloride ion. Here, I am confused about this. Any
> > kind of help will be highly appreciated.
>
> There are no covalent bonds in monoatomic ions, so any value of nrexcl
> can be used. NO3 has a maximum of two contiguous covalent bonds so
> nrexcl = 2. Or you can set nrexcl = 3 for everything, which has the
> exact same effect.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From snehasis.chatterjee18 at gmail.com  Sat Jan  4 07:38:28 2020
From: snehasis.chatterjee18 at gmail.com (Snehasis Chatterjee)
Date: Sat, 04 Jan 2020 06:38:28 -0000
Subject: [gmx-users] query regarding center of mass removal
In-Reply-To: <mailman.429.1578114096.1966.gromacs.org_gmx-users@maillist.sys.kth.se>
References: <mailman.429.1578114096.1966.gromacs.org_gmx-users@maillist.sys.kth.se>
Message-ID: <CAEScH65N+1L0NtLuM5BUv+AbPCFZSFjC+_03jm6+APuvGVFHEg@mail.gmail.com>

Thank you Prof. Lemkul for your kind reply. In mdp file, I will set
comm_grps to "system". But in tc-grps, can I couple capsid with Ca2+ ions?
240 Ca2+ ions are non-covalently attached with the capsid and have
important role in maintaining capsid stability.

I am also planing to run another set of simulation, where RNA is
non-covalently attached with the capsid. In tc-grps, I can couple capsid,
RNA and Ca2+ ions together. I am looking forward for your reply.

-Snehasis


On Sat, Jan 4, 2020 at 12:02 AM <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

> Send gromacs.org_gmx-users mailing list submissions to
>         gromacs.org_gmx-users at maillist.sys.kth.se
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or, via email, send a message with subject or body 'help' to
>         gromacs.org_gmx-users-request at maillist.sys.kth.se
>
> You can reach the person managing the list at
>         gromacs.org_gmx-users-owner at maillist.sys.kth.se
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
>    1. query regarding center of mass removal (Snehasis Chatterjee)
>    2. Re: query regarding center of mass removal (Justin Lemkul)
>    3. Re: What is the "gen-vel" used for? (Neena Susan Eappen)
>    4. Re: amide-capped C-terminus; OPLS force field (Neena Susan Eappen)
>    5. Re: nrexcl value for ions (Dhrubajyoti Maji)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 3 Jan 2020 15:29:49 -0500
> From: Snehasis Chatterjee <snehasis.chatterjee18 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] query regarding center of mass removal
> Message-ID:
>         <CAEScH66GPJ2cmUJPTAh0m2U=nhCmaG4HmTisXiR_sfv11Zr0=
> w at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear Gromacs users,
>
> I am trying to perform a virus capsid simulation using GROMACS 2018. 240
> Calcium ions bound to specific regions of the capsid and have important
> role in maintaining capsid stability. In this context, I had a query
> regarding the correct Center-of-Mass removal settings. I usually run
> protein simulation in aqueous environment using following mdp options:
>
>
>
> *nstcomm= 100comm_mode= linearcomm_grps= Protein Non-Protein*
>
> In aqueous environment, I typically use "Protein Non-Protein," with
> Non-Protein containing solvent and ions. Since, 240 Ca2+ ions are
> non-covalently attached with the capsid, I am planing to couple  capsid
> with Ca2+ ions. I am bit confused regarding this issue. Any kind of advice/
> suggestions will be deeply appreciated.
>
> Thanks in advance,
> Snehasis Chatterjee
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 3 Jan 2020 17:22:01 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] query regarding center of mass removal
> Message-ID: <0087bf32-f571-8dc4-0fc5-2e73c65af126 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 1/3/20 3:29 PM, Snehasis Chatterjee wrote:
> > Dear Gromacs users,
> >
> > I am trying to perform a virus capsid simulation using GROMACS 2018. 240
> > Calcium ions bound to specific regions of the capsid and have important
> > role in maintaining capsid stability. In this context, I had a query
> > regarding the correct Center-of-Mass removal settings. I usually run
> > protein simulation in aqueous environment using following mdp options:
> >
> >
> >
> > *nstcomm= 100comm_mode= linearcomm_grps= Protein Non-Protein*
> >
> > In aqueous environment, I typically use "Protein Non-Protein," with
> > Non-Protein containing solvent and ions. Since, 240 Ca2+ ions are
> > non-covalently attached with the capsid, I am planing to couple  capsid
> > with Ca2+ ions. I am bit confused regarding this issue. Any kind of
> advice/
> > suggestions will be deeply appreciated.
>
> For any system in an isotropic medium (i.e. water), comm-grps should be
> set to "system" because there are not multiple phases that may diffuse
> differently. You shouldn't use Protein/Non-Protein here; that's for
> tc-grps.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 3
> Date: Sat, 4 Jan 2020 02:11:21 +0000
> From: Neena Susan Eappen <neena.susaneappen at mail.utoronto.ca>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
>         <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] What is the "gen-vel" used for?
> Message-ID:
>         <
> YT1PR01MB37234D43C1489F79C11FAEADCD220 at YT1PR01MB3723.CANPRD01.PROD.OUTLOOK.COM
> >
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Yeping Sun,
>
> Quoting Justin's answer for a similar question I had on how to repeat a
> simulation say 10 times
>  " To run 10 independent simulations, I would run minimization once and
> start from 10 new equilibration runs, each with a different set of initial
> velocities (change gen_seed or simply set to -1).That approach may not be
> as robust as starting from 10 different configurations, but the exact
> approach depends on the system in question".
>
>
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Sat, 4 Jan 2020 02:36:39 +0000
> From: Neena Susan Eappen <neena.susaneappen at mail.utoronto.ca>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
>         <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] amide-capped C-terminus; OPLS force field
> Message-ID:
>         <
> YT1PR01MB3723BF41D44ED7648364E666CD220 at YT1PR01MB3723.CANPRD01.PROD.OUTLOOK.COM
> >
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> I do this by adding amide group at the C-terminus on Pymol, use -ter flag
> during gmx pdb2gmx command, select None (for C-terminus), N and H in that
> amide group are automatically recognized as atom types opls 237 and opls
> 240 respectively. The net charge of system remains neutral.
>
>
> ------------------------------
>
> Message: 5
> Date: Sat, 4 Jan 2020 10:31:21 +0530
> From: Dhrubajyoti Maji <dmaji43 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] nrexcl value for ions
> Message-ID:
>         <CACrPy4BsEr0AK9Nt-Tb=
> h8-feY+4DyypaS-TgRqg_ZBsK6fO5g at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Thank you Prof. Lemkul for your kind reply.
>
> Dhrubajyoti
>
> On Sat, 4 Jan 2020 at 01:01, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 1/3/20 12:10 AM, Dhrubajyoti Maji wrote:
> > > Dear gromacs users,
> > >       A very happy new year to all of you. I an trying to simulate LiBr
> > and
> > > LiNO3. What will be the value of nrexcl in OPLS itp file for respective
> > > cation and anions? I found nrexcl=1 for atomic ions in ions.itp file in
> > > gromacs. Again in a tutorial of simulation of Choline Chloride + urea,
> > they
> > > have used nrecxl=3 for chloride ion. Here, I am confused about this.
> Any
> > > kind of help will be highly appreciated.
> >
> > There are no covalent bonds in monoatomic ions, so any value of nrexcl
> > can be used. NO3 has a maximum of two contiguous covalent bonds so
> > nrexcl = 2. Or you can set nrexcl = 3 for everything, which has the
> > exact same effect.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Office: 301 Fralin Hall
> > Lab: 303 Engel Hall
> >
> > Virginia Tech Department of Biochemistry
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.thelemkullab.com
> >
> > ==================================================
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 189, Issue 7
> *****************************************************
>

From majid_rezaei66 at yahoo.com  Sat Jan  4 13:44:12 2020
From: majid_rezaei66 at yahoo.com (Majid Rezaei)
Date: Sat, 04 Jan 2020 12:44:12 -0000
Subject: [gmx-users] The pull code
References: <732286252.7931813.1578141846599.ref@mail.yahoo.com>
Message-ID: <732286252.7931813.1578141846599@mail.yahoo.com>

Dear gromacs users,
I am tryingto make a shear flow in an electrolyte by moving two parallel bilayers immersedin the electrolyte in opposite directions. I use the following pull code (wherethe groups low and up are the two moving bilayers):
pull?= yespull-coord1-type?= umbrellapull-coord1-geometry= direction-periodicpull-pbc-ref-prev-step-com= yespull-coord1-dim?= Y N Npull-coord1-vec??? = 1 0 0pull-coord1-start? = yespull-ngroups?= 2pull-group1-name?= lowpull-group1-pbcatom= 2pull-group2-name?= uppull-group2-pbcatom= 1202pull-coord1-groups= 1 2pull-coord1-rate?? = 0.030?pull-coord1-k?= 500? ?pull-coord1-init?? = 1.3pull-nstxout?= 250pull-nstfout?= 250
I expect thevelocity of the bilayers to be ?15 m/s. But the calculated velocityprofile shows a velocity of around 5 m/s. I also tried some other rates ofchange of the reference position and found that the calculated velocity isalways around 3 times less than what I expect. Could you please let me know whatis the problem with my code?
?It shouldbe noted that I am using Gromacs 2019 and that I didn?t encounter such problemwhen using the same code (minus the pull-pbc-ref-prev-step-comcommand) and the same simulation system in Gromacs 2016?
Best wishes,Majid

From shakirashukoor1993 at gmail.com  Sat Jan  4 16:25:04 2020
From: shakirashukoor1993 at gmail.com (shakira shukoor)
Date: Sat, 04 Jan 2020 15:25:04 -0000
Subject: [gmx-users] GROMOS forcefields
Message-ID: <CADV28mcCVN-FQaN0mLx3PFmdg0A8=35VYJbdYgUQMw2TsxeDDw@mail.gmail.com>

Hi all
Can anyone explain the different code seen in forcefields of GROMOS like
53A6, 54A7, 43a1,..... what does these numbers mean?

-- 
*Best Regards*

Shakkira E
PhD student INSPIRE Scholar
Department of Chemistry
sdmdlab.xyz
IIT Patna
Bihta
Patna 801106

From goossens_kenny at hotmail.com  Sat Jan  4 17:29:41 2020
From: goossens_kenny at hotmail.com (Kenny Goossens)
Date: Sat, 04 Jan 2020 16:29:41 -0000
Subject: [gmx-users] GROMOS forcefields
In-Reply-To: <CADV28mcCVN-FQaN0mLx3PFmdg0A8=35VYJbdYgUQMw2TsxeDDw@mail.gmail.com>
References: <CADV28mcCVN-FQaN0mLx3PFmdg0A8=35VYJbdYgUQMw2TsxeDDw@mail.gmail.com>
Message-ID: <AM0PR01MB651427B7C0D17D0631FA1B8FF8220@AM0PR01MB6514.eurprd01.prod.exchangelabs.com>

Hi Shakkira,

In each of the consecutice iterations of the GROMOS force field, a reparameterization of the constants was performed in order to reproduce experimental data for various molecules (in the case of the GROMOS suite, parameterization is mainly fitted to free enthalpy of solvation). For GROMOS54a7, the focus was on improving behaviour of amino acids. Older iterations of the force field have less parameters, and are in general less accurate. This depends on the system you are working with, however. The first number (43,56,...) stands for the number of atom types in the force field, the last number stands for the iteration of the force field. Also not that A and B versions are designed for different types of applications.

I would advise you to look into the literature on the parameterization of the force fields to get an idea of the improvements/changes in every iteration of the force field. Furthermore, beware as the GROMOS force field does not always show the intended behavior in newer versions of Gromacs, and extra caution has to be taken in deciding on the simulation conditions. The issues are illustrated i.e. in Rei?er 2017m JCTC (10.1021/acs.jctc.7b00178) And Silva et al 2018 JCTC (10.1021/acs.jctc.8b00758). As far as I'm aware, the Gromacs team has decided to discontinue support for GROMOS in the future for this reason.

With kind regards,
______________________________
Kenneth Goossens, PhD student
Laboratory of Medicinal Chemistry (Building A - Room 2.13)
University of Antwerp - Campus Drie Eiken
Universiteitsplein 1
B-2610 Wilrijk
Belgium


________________________________
Van: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> namens shakira shukoor <shakirashukoor1993 at gmail.com>
Verzonden: zaterdag 4 januari 2020 16:23
Aan: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
Onderwerp: [gmx-users] GROMOS forcefields

Hi all
Can anyone explain the different code seen in forcefields of GROMOS like
53A6, 54A7, 43a1,..... what does these numbers mean?

--
*Best Regards*

Shakkira E
PhD student INSPIRE Scholar
Department of Chemistry
sdmdlab.xyz
IIT Patna
Bihta
Patna 801106
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

From navneetcdl at gmail.com  Sat Jan  4 17:43:29 2020
From: navneetcdl at gmail.com (Navneet Kumar)
Date: Sat, 04 Jan 2020 16:43:29 -0000
Subject: [gmx-users] GROMOS forcefields
In-Reply-To: <AM0PR01MB651427B7C0D17D0631FA1B8FF8220@AM0PR01MB6514.eurprd01.prod.exchangelabs.com>
References: <CADV28mcCVN-FQaN0mLx3PFmdg0A8=35VYJbdYgUQMw2TsxeDDw@mail.gmail.com>
	<AM0PR01MB651427B7C0D17D0631FA1B8FF8220@AM0PR01MB6514.eurprd01.prod.exchangelabs.com>
Message-ID: <CAOvdM4UCWh4uNe4wgRD_G3dxnty6+5OjzN-k0WLh29bbF=Bfow@mail.gmail.com>

Very informative and interesting. I was using 54a7 forcefield with GROMACS
2018.4. I was confused with mdp parameters. Which version of GROMACS should
I use if I want to employ 54a7 force field?

On Sat, 4 Jan 2020, 22:00 Kenny Goossens, <goossens_kenny at hotmail.com>
wrote:

> Hi Shakkira,
>
> In each of the consecutice iterations of the GROMOS force field, a
> reparameterization of the constants was performed in order to reproduce
> experimental data for various molecules (in the case of the GROMOS suite,
> parameterization is mainly fitted to free enthalpy of solvation). For
> GROMOS54a7, the focus was on improving behaviour of amino acids. Older
> iterations of the force field have less parameters, and are in general less
> accurate. This depends on the system you are working with, however. The
> first number (43,56,...) stands for the number of atom types in the force
> field, the last number stands for the iteration of the force field. Also
> not that A and B versions are designed for different types of applications.
>
> I would advise you to look into the literature on the parameterization of
> the force fields to get an idea of the improvements/changes in every
> iteration of the force field. Furthermore, beware as the GROMOS force field
> does not always show the intended behavior in newer versions of Gromacs,
> and extra caution has to be taken in deciding on the simulation conditions.
> The issues are illustrated i.e. in Rei?er 2017m JCTC
> (10.1021/acs.jctc.7b00178) And Silva et al 2018 JCTC
> (10.1021/acs.jctc.8b00758). As far as I'm aware, the Gromacs team has
> decided to discontinue support for GROMOS in the future for this reason.
>
> With kind regards,
> ______________________________
> Kenneth Goossens, PhD student
> Laboratory of Medicinal Chemistry (Building A - Room 2.13)
> University of Antwerp - Campus Drie Eiken
> Universiteitsplein 1
> B-2610 Wilrijk
> Belgium
>
>
> ________________________________
> Van: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> namens shakira shukoor
> <shakirashukoor1993 at gmail.com>
> Verzonden: zaterdag 4 januari 2020 16:23
> Aan: gromacs.org_gmx-users at maillist.sys.kth.se <
> gromacs.org_gmx-users at maillist.sys.kth.se>
> Onderwerp: [gmx-users] GROMOS forcefields
>
> Hi all
> Can anyone explain the different code seen in forcefields of GROMOS like
> 53A6, 54A7, 43a1,..... what does these numbers mean?
>
> --
> *Best Regards*
>
> Shakkira E
> PhD student INSPIRE Scholar
> Department of Chemistry
> sdmdlab.xyz
> IIT Patna
> Bihta
> Patna 801106
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From jalemkul at vt.edu  Sat Jan  4 17:44:06 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Sat, 04 Jan 2020 16:44:06 -0000
Subject: [gmx-users] GROMOS forcefields
In-Reply-To: <AM0PR01MB651427B7C0D17D0631FA1B8FF8220@AM0PR01MB6514.eurprd01.prod.exchangelabs.com>
References: <CADV28mcCVN-FQaN0mLx3PFmdg0A8=35VYJbdYgUQMw2TsxeDDw@mail.gmail.com>
	<AM0PR01MB651427B7C0D17D0631FA1B8FF8220@AM0PR01MB6514.eurprd01.prod.exchangelabs.com>
Message-ID: <9020dd94-f4b6-ffcf-fb42-99a6a1802e51@vt.edu>



On 1/4/20 11:29 AM, Kenny Goossens wrote:
> Hi Shakkira,
>
> In each of the consecutice iterations of the GROMOS force field, a reparameterization of the constants was performed in order to reproduce experimental data for various molecules (in the case of the GROMOS suite, parameterization is mainly fitted to free enthalpy of solvation). For GROMOS54a7, the focus was on improving behaviour of amino acids. Older iterations of the force field have less parameters, and are in general less accurate. This depends on the system you are working with, however. The first number (43,56,...) stands for the number of atom types in the force field, the last number stands for the iteration of the force field. Also not that A and B versions are designed for different types of applications.
>
> I would advise you to look into the literature on the parameterization of the force fields to get an idea of the improvements/changes in every iteration of the force field. Furthermore, beware as the GROMOS force field does not always show the intended behavior in newer versions of Gromacs, and extra caution has to be taken in deciding on the simulation conditions. The issues are illustrated i.e. in Rei?er 2017m JCTC (10.1021/acs.jctc.7b00178) And Silva et al 2018 JCTC (10.1021/acs.jctc.8b00758). As far as I'm aware, the Gromacs team has decided to discontinue support for GROMOS in the future for this reason.

Another 2018 paper accused GROMACS of being buggy: 
https://pubs.acs.org/doi/10.1021/acs.jctc.8b00425 - that study has 
motivated the response from the core GROMACS developers 
(https://chemrxiv.org/articles/On_The_Importance_of_Accurate_Algorithms_for_Reliable_Molecular_Dynamics_Simulations/11474583/1) 
illustrating defects in the physical model used to derive many of the 
the GROMOS parameter sets; it's not a bug in GROMACS that is likely the 
issue.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From jalemkul at vt.edu  Sat Jan  4 17:44:42 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Sat, 04 Jan 2020 16:44:42 -0000
Subject: [gmx-users] query regarding center of mass removal
In-Reply-To: <CAEScH65N+1L0NtLuM5BUv+AbPCFZSFjC+_03jm6+APuvGVFHEg@mail.gmail.com>
References: <mailman.429.1578114096.1966.gromacs.org_gmx-users@maillist.sys.kth.se>
	<CAEScH65N+1L0NtLuM5BUv+AbPCFZSFjC+_03jm6+APuvGVFHEg@mail.gmail.com>
Message-ID: <0878fb58-617a-7496-6dc6-bbf871fb5e24@vt.edu>



On 1/4/20 1:38 AM, Snehasis Chatterjee wrote:
> Thank you Prof. Lemkul for your kind reply. In mdp file, I will set
> comm_grps to "system". But in tc-grps, can I couple capsid with Ca2+ ions?
> 240 Ca2+ ions are non-covalently attached with the capsid and have
> important role in maintaining capsid stability.
>
> I am also planing to run another set of simulation, where RNA is
> non-covalently attached with the capsid. In tc-grps, I can couple capsid,
> RNA and Ca2+ ions together. I am looking forward for your reply.

Generally solute and solvent are coupled separately, however you define 
what the solute is.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From paul.bauer.q at gmail.com  Sat Jan  4 18:55:26 2020
From: paul.bauer.q at gmail.com (Paul bauer)
Date: Sat, 04 Jan 2020 17:55:26 -0000
Subject: [gmx-users] GROMACS 2020 official release
In-Reply-To: <f7408a41-9e20-52aa-1220-310723cc46cc@gmail.com>
References: <f7408a41-9e20-52aa-1220-310723cc46cc@gmail.com>
Message-ID: <eb4be3df-b09c-3691-22fd-3666ec93bbaa@gmail.com>

Hello again,

I got notified that there is an issue for the first link, it needs to be 
without the final dot:

http://manual.gromacs.org/2020/release-notes/index.html

Sorry for the inconvenience and happy new year!

Cheers

Paul

On 01/01/2020 18:11, Paul bauer wrote:
> Hello GROMACS users!
>
> The official release of GROMACS 2020 is now available.
>
> What new things can you expect? Please see the release notes 
> highlights at
> http://manual.gromacs.org/2020/release-notes/index.html.
>
> You can find the code, manual, release notes, installation 
> instructions and
> test suite at the links below.
>
> Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2020.tar.gz
> Documentation: http://manual.gromacs.org/2020/index.html
> (includes install guide, user guide, reference manual, and release notes)
> Test Suite: 
> http://gerrit.gromacs.org/download/regressiontests-2020.tar.gz
>
> Happy simulating!
>

-- 
Paul Bauer, PhD
GROMACS Development Manager
KTH Stockholm, SciLifeLab
0046737308594


From profiles.ke at gmail.com  Sat Jan  4 19:17:58 2020
From: profiles.ke at gmail.com (Quin K)
Date: Sat, 04 Jan 2020 18:17:58 -0000
Subject: [gmx-users] [gmx-user] Autodock Vina Out use in gromacs MD
In-Reply-To: <921bd165-2e24-4e27-9664-b2f5bd382f72@vt.edu>
References: <CAG0e8MMkVer9b8NEvQoduajr3ggFVkXJW6_C-L+9cqB-SimUJQ@mail.gmail.com>
	<CAG0e8MM+Ep=ptOhmCN4XKymbmBXcCQV6GcvE-CsmTvgY8NwdoA@mail.gmail.com>
	<921bd165-2e24-4e27-9664-b2f5bd382f72@vt.edu>
Message-ID: <CAG0e8MP5V6ts7TJMf3ZjT=tH5gHcyxjymE0iqVPqOafg3LJC7A@mail.gmail.com>

Dear Proffesor Lemkul,

I have given below the MD RMSD for complex, and noted that Ligand is
getting detached again. When I viewed the trajectory on VMD it was
confirmed.  The ligand did not abruptly got dislodged instead it slowly
came out of binding pocket and started moving around after.
https://drive.google.com/file/d/1IBMU-8SzSgXVr_h9zyeVwNV7kQ4at8-S/view?usp=sharing

I know that following CGenFF tutorial and fixing the molecule and
reparameterization would be the correct thing to do however I lack time at
this moment.
I read the paper and went through the tutorial and it's some what of a
complex method to fix the parameters.
I was thinking if I should use a different force-field such as Gromos with
parameterization with ATB server.
I have already submitted the given molecule below for optimization in ATB
and the parameterization is now complete.
Other option is to use Amber force field. Kindly let me know what your
opinion on this.

Molecule
https://drive.google.com/file/d/1Ni8rUX4sH3aKaRhhXqCZr9w8VJVetCI7/view?usp=sharing

Interactions at binding site us DS Visualizer
https://drive.google.com/file/d/16EkWYDPDyTfkERiQgaOYo4XxYxqslOD0/view?usp=sharing

Also please let me know if you think the given interactions are enough to
keep the molecule at binding site for like 100ns?

Thank you in Advance!
Kind Regards
Q

On Tue, Dec 31, 2019 at 9:21 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/30/19 1:51 PM, Quin K wrote:
> > Further to following email, is it OK to do an energy minimization with
> > Gaussian16 so the molecule is refined before MD simulation with Gromacs?
>
> What would be the purpose? A gas-phase optimized geometry has no
> relationship to the pose adopted by a molecule upon binding to its
> receptor.
>
> > If such an energy minimization is done should I use DFT ?
>
> Depends on the force field you're using. Most biomolecular force fields
> do not use DFT for most calculations. If this goes back to our original
> discussion about your CGenFF parameters, I beg you to follow the advice
> I already gave - read the CGenFF paper. It tells you the *exact* model
> chemistries you should use for everything to ensure compatibility with
> the CHARMM force field.
>
> > Would that affect the orientation at which molecule was docked with
> > protein?
>
> No, because the docking software changes the configuration.
>
> -Justin
>
> >
> > On Mon, Dec 30, 2019 at 8:35 PM Quin K <profiles.ke at gmail.com> wrote:
> >
> >> Hi
> >>
> >> I noted when I used Autodock vina for docking and used the converted
> back
> >> .mol2 file from .pdbqt format, there were a lot of changes in the
> molecule
> >> than the molecule I initially submitted to Vina for docking. Like the
> *atomic
> >> charges were different. *
> >> Is this normal? or is there a way to use the original DFT optimized
> >> molecule with current docking orientation of Vina output file??
> >> Also noted that there were missing atoms like hydrogens.
> >> Last time I tried this simulation the ligand got detached from binding
> >> site after like 20 ns. This could probably be a main reason for that
> >> because I never refined the molecule to adjust for changed charges etc.
> >>
> >> Kindly give your opinion
> >> Thanks!
> >> Regards!
> >>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From shakirashukoor1993 at gmail.com  Sat Jan  4 19:43:26 2020
From: shakirashukoor1993 at gmail.com (shakira shukoor)
Date: Sat, 04 Jan 2020 18:43:26 -0000
Subject: [gmx-users] GROMOS forcefields
In-Reply-To: <AM0PR01MB651427B7C0D17D0631FA1B8FF8220@AM0PR01MB6514.eurprd01.prod.exchangelabs.com>
References: <CADV28mcCVN-FQaN0mLx3PFmdg0A8=35VYJbdYgUQMw2TsxeDDw@mail.gmail.com>
	<AM0PR01MB651427B7C0D17D0631FA1B8FF8220@AM0PR01MB6514.eurprd01.prod.exchangelabs.com>
Message-ID: <CADV28mdfy33hBYiqGoPuRhf=xNomUS4Vn8BPTaMsmM4-s9gJWg@mail.gmail.com>

Thank you for such a detailed response. The explanation was very helpful.

On Sat, Jan 4, 2020 at 10:00 PM Kenny Goossens <goossens_kenny at hotmail.com>
wrote:

> Hi Shakkira,
>
> In each of the consecutice iterations of the GROMOS force field, a
> reparameterization of the constants was performed in order to reproduce
> experimental data for various molecules (in the case of the GROMOS suite,
> parameterization is mainly fitted to free enthalpy of solvation). For
> GROMOS54a7, the focus was on improving behaviour of amino acids. Older
> iterations of the force field have less parameters, and are in general less
> accurate. This depends on the system you are working with, however. The
> first number (43,56,...) stands for the number of atom types in the force
> field, the last number stands for the iteration of the force field. Also
> not that A and B versions are designed for different types of applications.
>
> I would advise you to look into the literature on the parameterization of
> the force fields to get an idea of the improvements/changes in every
> iteration of the force field. Furthermore, beware as the GROMOS force field
> does not always show the intended behavior in newer versions of Gromacs,
> and extra caution has to be taken in deciding on the simulation conditions.
> The issues are illustrated i.e. in Rei?er 2017m JCTC
> (10.1021/acs.jctc.7b00178) And Silva et al 2018 JCTC
> (10.1021/acs.jctc.8b00758). As far as I'm aware, the Gromacs team has
> decided to discontinue support for GROMOS in the future for this reason.
>
> With kind regards,
> ______________________________
> Kenneth Goossens, PhD student
> Laboratory of Medicinal Chemistry (Building A - Room 2.13)
> University of Antwerp - Campus Drie Eiken
> Universiteitsplein 1
> B-2610 Wilrijk
> Belgium
>
>
> ________________________________
> Van: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> namens shakira shukoor
> <shakirashukoor1993 at gmail.com>
> Verzonden: zaterdag 4 januari 2020 16:23
> Aan: gromacs.org_gmx-users at maillist.sys.kth.se <
> gromacs.org_gmx-users at maillist.sys.kth.se>
> Onderwerp: [gmx-users] GROMOS forcefields
>
> Hi all
> Can anyone explain the different code seen in forcefields of GROMOS like
> 53A6, 54A7, 43a1,..... what does these numbers mean?
>
> --
> *Best Regards*
>
> Shakkira E
> PhD student INSPIRE Scholar
> Department of Chemistry
> sdmdlab.xyz
> IIT Patna
> Bihta
> Patna 801106
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>


-- 
*Best Regards*

Shakkira E
PhD student INSPIRE Scholar
Department of Chemistry
sdmdlab.xyz
IIT Patna
Bihta
Patna 801106

From kevin.boyd at uconn.edu  Sat Jan  4 21:11:28 2020
From: kevin.boyd at uconn.edu (Kevin Boyd)
Date: Sat, 04 Jan 2020 20:11:28 -0000
Subject: [gmx-users] Gromacs 2019 - Ryzen Architecture
In-Reply-To: <44a30732-2788-f60e-ecca-58959a63dc19@gmail.com>
References: <2f123e28-d6bb-4958-8eab-85f8a1158a14@fu-berlin.de>
	<44a30732-2788-f60e-ecca-58959a63dc19@gmail.com>
Message-ID: <CAEJMVeum9CB9ygf9r36F9+C8bXCwL2GuCpgVJBo648YO1eS8dw@mail.gmail.com>

Hi,

A few things besides any Ryzen-specific issues. First, your pinoffset for
the second one should be 16, not 17. The way yours is set up, you're
running on cores 0-15, then Gromacs will detect that your second
simulation parameters are invalid (because from cores 17-32, core 32 does
not exist) and turn off core pinning. You can verify that in the log file.

Second, 16 threads per simulation is overkill, and you can get gains from
stealing from GPU down-time by running 2 simulations per GPU. So I would
suggest something like

mdrun -nt 8 -pin on -pinoffset 0 -gpu_id 0 &
mdrun -nt 8 -pin on -pinoffset 8 -gpu_id 0 &
mdrun -nt 8 -pin on -pinoffset 16 -gpu_id 1 &
mdrun -nt 8 -pin on -pinoffset 24 -gpu_id 1

might give you close to optimal performance.

On Thu, Jan 2, 2020 at 5:32 AM Paul bauer <paul.bauer.q at gmail.com> wrote:

> Hello,
>
> we only added full detection and support for the newer Rizen chip-sets
> with GROMACS 2019.5, so please try if the update to this version solves
> your issue.
> If not, please open an issue on redmine.gromacs.org so we can track the
> problem and try to solve it.
>
> Cheers
>
> Paul
>
> On 02/01/2020 13:26, Sandro Wrzalek wrote:
> > Hi,
> >
> > happy new year!
> >
> > Now to my problem:
> >
> > I use Gromacs 2019.3 and to try to run some simulations (roughly 30k
> > atoms per system) on my PC which has the following configuration:
> >
> > CPU: Ryzen 3950X (overclocked to 4.1 GHz)
> >
> > GPU #1: Nvidia RTX 2080 Ti
> >
> > GPU #2: Nvidia RTX 2080 Ti
> >
> > RAM: 64 GB
> >
> > PSU: 1600 Watts
> >
> >
> > Each run uses one GPU and 16 of 32 logical cores. Doing only one run
> > at time (gmx mdrun -deffnm rna0 -gpu_id 0 -nb gpu -pme gpu) the GPU
> > utilization is roughly around 84% but if I add a second run, the
> > utilization of both GPUs drops to roughly 20%, while leaving logical
> > cores 17-32 idle (I changed parameter gpu_id, accordingly).
> >
> > Adding additional parameters for each run:
> >
> > gmx mdrun -deffnm rna0 -nt 16 -pin on -pinoffset 0 -gpu_id 0 -nb gpu
> > -pme gpu
> >
> > gmx mdrun -deffnm rna0 -nt 16 -pin on -pinoffset 17 -gpu_id 1 -nb gpu
> > -pme gpu
> >
> > I get a utilization of 78% per GPU, which is nice but not near the 84%
> > I got with only one run. In theory, however, it should come at least
> > close to that utilization.
> >
> > I suspect, the Ryzen Chiplet design as the culprit since Gromacs seems
> > to prefer the the first Chiplet, even if two simultaneous simulations
> > have the resources to occupy both. The reason for the 78% utilization
> > could be because of overhead between the two Chiplets via the infinity
> > band. However, I have no proof, nor am I able to explain why gmx mdrun
> > -deffnm rna0 -nt 16 -gpu_id 0 & 1 -nb gpu -pme gpu works as well -
> > seems to occupy free logical cores then.
> >
> > Long story short:
> >
> > Are there any workarounds to squeeze the last bit out of my setup? Is
> > it possible to choose the logical cores manually (I did not found
> > anything in the docs so far)?
> >
> >
> > Thank you for your help!
> >
> >
> > Best,
> >
> > Sandro
> >
>
> --
> Paul Bauer, PhD
> GROMACS Development Manager
> KTH Stockholm, SciLifeLab
> 0046737308594
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From kevin.boyd at uconn.edu  Sat Jan  4 21:14:12 2020
From: kevin.boyd at uconn.edu (Kevin Boyd)
Date: Sat, 04 Jan 2020 20:14:12 -0000
Subject: [gmx-users] Bilayer exploding with semiisotropic coupling
In-Reply-To: <CANTDrdHUxxgzCnF=_vFeELn3cfBoZYfEY4QOXHprt_UyHs5Eyw@mail.gmail.com>
References: <CANTDrdHmTKV1VOoW9=2A2z8U4_BLbdtVgLaCo0SU6iH=RYCftQ@mail.gmail.com>
	<CANTDrdHUxxgzCnF=_vFeELn3cfBoZYfEY4QOXHprt_UyHs5Eyw@mail.gmail.com>
Message-ID: <CAEJMVesftqdyATJdtNhXHwL_8esGN_UvZMrFcKGbFxbhi9SR0A@mail.gmail.com>

Hi,

Can you share more information? Please upload your starting configuration
and a log file.

On Fri, Jan 3, 2020 at 10:29 AM Namit Chaudhary <nchaudha at andrew.cmu.edu>
wrote:

> Hi,
>
> Sorry. I didn't realize that attachments aren't uploaded. Below is a link
> for the files mentioned in the original mail.
>
> https://drive.google.com/drive/folders/1fUrx4yt3DpCEGY0CACA6n-PXcswfaa31?usp=sharing
>
> Namit
>
> On Fri, Jan 3, 2020 at 1:12 PM Namit Chaudhary <nchaudha at andrew.cmu.edu>
> wrote:
>
> > Hi all,
> >
> > I am trying to simulate a coarse grain system containing DPPC (10%),
> > Cholesterol (40%) and a custom lipid that's synthesized by our lab (50%,
> > topology and martini mapping attached).  Our lab uses these molecules to
> > formulate lipid nanoparticles and deliver RNA therapeutics. I am trying
> to
> > understand the structure of these nanoparticles. I tried modelling them
> as
> > a bilayer but the system seems to be exploding in the z - direction
> during
> > the production run if I use semiisotropic or anisotropic pressure
> coupling
> > (isotropic coupling seems to work).  Below is the md.mdp file that I am
> > using.
> >
> > integrator               = md
> > dt                           = 0.01
> > nsteps                   = 8000000
> > nstcomm               = 100
> > comm-grps            = LIPIDS SOL
> >
> >
> > nstxout                  = 0
> > nstvout                  = 0
> > nstfout                  = 0
> > nstlog                   = 1000  ; Output frequency for energies to log
> > file
> > nstenergy                = 100   ; Output frequency for energies to
> energy
> > file
> > nstxtcout                = 1000  ; Output frequency for .xtc file
> > xtc_precision            = 100
> > xtc-grps                 =
> > energygrps               =
> >
> >
> > nstlist                  = 10
> > ns_type                  = grid
> > pbc                      = xyz
> > rlist                    = 1.1
> >
> > coulombtype              = reaction_field  ;Reaction_field (for use with
> > Verlet-pairlist) ;PME (especially with polarizable water)
> > rcoulomb_switch          = 0.0
> > rcoulomb                 = 1.1
> > epsilon_r                = 15 ; 2.5 (with polarizable water)
> > vdw_type                 = cutoff  ;cutoff (for use with Verlet-pairlist)
> >
> > rvdw_switch              = 0.9
> > rvdw                     = 1.1 ;1.1 (for use with Verlet-pairlist)
> >
> > cutoff-scheme            = verlet
> >
> > tcoupl                   = v-rescale
> > tc-grps                  = LIPIDS SOL
> > tau_t                     = 1.0  1.0
> > ref_t                      = 298 298
> > Pcoupl                   = parrinello-rahman
> > Pcoupltype            = semiisotropic
> > tau_p                     = 12.0
> > compressibility       = 3e-4 3e-4      ; 3e-4
> > ref_p                      = 1.0 1.0       ; 1.0 1.0
> >
> > gen_vel                    = yes
> > gen_temp                 = 298
> > gen_seed                 = 473529
> >
> > constraints                = none
> > constraint_algorithm = Lincs
> > continuation              = no
> > lincs_order                = 4
> > lincs_warnangle        = 30
> >
> > Is there something that I can change in my mdp file? Or is there
> something
> > wrong with the lipid itself?
> >
> >
> > Thank you
> > Namit
> >
>
>
> --
> *Namit Chaudhary*
> Chemical Engineering | Carnegie Mellon University
> M: 724-506-0693 | E: nchaudha at andrew.cmu.edu
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From paul.bauer.q at gmail.com  Sat Jan  4 21:17:29 2020
From: paul.bauer.q at gmail.com (Paul Bauer)
Date: Sat, 04 Jan 2020 20:17:29 -0000
Subject: [gmx-users] Bilayer exploding with semiisotropic coupling
In-Reply-To: <CAEJMVesftqdyATJdtNhXHwL_8esGN_UvZMrFcKGbFxbhi9SR0A@mail.gmail.com>
References: <CANTDrdHmTKV1VOoW9=2A2z8U4_BLbdtVgLaCo0SU6iH=RYCftQ@mail.gmail.com>
	<CANTDrdHUxxgzCnF=_vFeELn3cfBoZYfEY4QOXHprt_UyHs5Eyw@mail.gmail.com>
	<CAEJMVesftqdyATJdtNhXHwL_8esGN_UvZMrFcKGbFxbhi9SR0A@mail.gmail.com>
Message-ID: <CAKcZa822PX5mGaNyFQVDOYnCPWmVdvk9nJ=Li3TLSGMoBXt0Dw@mail.gmail.com>

Hello,

please upload the log file from the run, as well as the command you used to
run the simulation and your system specs (processor, whether you are using
GPUs).

Then we can see what is wrong here.

Thanks in advance.

Cheers

Paul

On Sat, 4 Jan 2020, 21:14 Kevin Boyd, <kevin.boyd at uconn.edu> wrote:

> Hi,
>
> Can you share more information? Please upload your starting configuration
> and a log file.
>
> On Fri, Jan 3, 2020 at 10:29 AM Namit Chaudhary <nchaudha at andrew.cmu.edu>
> wrote:
>
> > Hi,
> >
> > Sorry. I didn't realize that attachments aren't uploaded. Below is a link
> > for the files mentioned in the original mail.
> >
> >
> https://drive.google.com/drive/folders/1fUrx4yt3DpCEGY0CACA6n-PXcswfaa31?usp=sharing
> >
> > Namit
> >
> > On Fri, Jan 3, 2020 at 1:12 PM Namit Chaudhary <nchaudha at andrew.cmu.edu>
> > wrote:
> >
> > > Hi all,
> > >
> > > I am trying to simulate a coarse grain system containing DPPC (10%),
> > > Cholesterol (40%) and a custom lipid that's synthesized by our lab
> (50%,
> > > topology and martini mapping attached).  Our lab uses these molecules
> to
> > > formulate lipid nanoparticles and deliver RNA therapeutics. I am trying
> > to
> > > understand the structure of these nanoparticles. I tried modelling them
> > as
> > > a bilayer but the system seems to be exploding in the z - direction
> > during
> > > the production run if I use semiisotropic or anisotropic pressure
> > coupling
> > > (isotropic coupling seems to work).  Below is the md.mdp file that I am
> > > using.
> > >
> > > integrator               = md
> > > dt                           = 0.01
> > > nsteps                   = 8000000
> > > nstcomm               = 100
> > > comm-grps            = LIPIDS SOL
> > >
> > >
> > > nstxout                  = 0
> > > nstvout                  = 0
> > > nstfout                  = 0
> > > nstlog                   = 1000  ; Output frequency for energies to log
> > > file
> > > nstenergy                = 100   ; Output frequency for energies to
> > energy
> > > file
> > > nstxtcout                = 1000  ; Output frequency for .xtc file
> > > xtc_precision            = 100
> > > xtc-grps                 =
> > > energygrps               =
> > >
> > >
> > > nstlist                  = 10
> > > ns_type                  = grid
> > > pbc                      = xyz
> > > rlist                    = 1.1
> > >
> > > coulombtype              = reaction_field  ;Reaction_field (for use
> with
> > > Verlet-pairlist) ;PME (especially with polarizable water)
> > > rcoulomb_switch          = 0.0
> > > rcoulomb                 = 1.1
> > > epsilon_r                = 15 ; 2.5 (with polarizable water)
> > > vdw_type                 = cutoff  ;cutoff (for use with
> Verlet-pairlist)
> > >
> > > rvdw_switch              = 0.9
> > > rvdw                     = 1.1 ;1.1 (for use with Verlet-pairlist)
> > >
> > > cutoff-scheme            = verlet
> > >
> > > tcoupl                   = v-rescale
> > > tc-grps                  = LIPIDS SOL
> > > tau_t                     = 1.0  1.0
> > > ref_t                      = 298 298
> > > Pcoupl                   = parrinello-rahman
> > > Pcoupltype            = semiisotropic
> > > tau_p                     = 12.0
> > > compressibility       = 3e-4 3e-4      ; 3e-4
> > > ref_p                      = 1.0 1.0       ; 1.0 1.0
> > >
> > > gen_vel                    = yes
> > > gen_temp                 = 298
> > > gen_seed                 = 473529
> > >
> > > constraints                = none
> > > constraint_algorithm = Lincs
> > > continuation              = no
> > > lincs_order                = 4
> > > lincs_warnangle        = 30
> > >
> > > Is there something that I can change in my mdp file? Or is there
> > something
> > > wrong with the lipid itself?
> > >
> > >
> > > Thank you
> > > Namit
> > >
> >
> >
> > --
> > *Namit Chaudhary*
> > Chemical Engineering | Carnegie Mellon University
> > M: 724-506-0693 | E: nchaudha at andrew.cmu.edu
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From nchaudha at andrew.cmu.edu  Sun Jan  5 12:55:33 2020
From: nchaudha at andrew.cmu.edu (Namit Chaudhary)
Date: Sun, 05 Jan 2020 11:55:33 -0000
Subject: [gmx-users] Bilayer exploding with semiisotropic coupling
In-Reply-To: <CANTDrdHUxxgzCnF=_vFeELn3cfBoZYfEY4QOXHprt_UyHs5Eyw@mail.gmail.com>
References: <CANTDrdHmTKV1VOoW9=2A2z8U4_BLbdtVgLaCo0SU6iH=RYCftQ@mail.gmail.com>
	<CANTDrdHUxxgzCnF=_vFeELn3cfBoZYfEY4QOXHprt_UyHs5Eyw@mail.gmail.com>
Message-ID: <CANTDrdFOba3OQf5ffrkfP2SeYQ+==NgnbP-A+SWNgqyMkCxX0g@mail.gmail.com>

Hi,

I have added the energy minimization, npt and the final run log, edr and
mdp files in the drive folder. Here's the link again:

https://drive.google.com/drive/folders/1fUrx4yt3DpCEGY0CACA6n-PXcswfaa31?usp=sharing

I am prepping everything up to npt equilibration on my laptop. It has a
Intel i7-7820 HQ processor and a GEForce 940MX GPU. The production run is
done on another computer that has an Intel i7-8700K processor and a GTX
1080Ti and GTX 1060 GPUs. Both GPUs are used for the production run.

I use gmx mdrun -v -deffnm {filename} for the production run.

Hope these are helpful. Please let me know if any other information is
required.

Thank you
Namit

From neena.susaneappen at mail.utoronto.ca  Sun Jan  5 21:43:54 2020
From: neena.susaneappen at mail.utoronto.ca (Neena Susan Eappen)
Date: Sun, 05 Jan 2020 20:43:54 -0000
Subject: [gmx-users]  Simulated Annealing command line
Message-ID: <YT1PR01MB37230F186B52FAD60AD177CFCD3D0@YT1PR01MB3723.CANPRD01.PROD.OUTLOOK.COM>

Hello gromacs users,

For simulated annealing, I want to repeat cycle (equilibration, annealing, production run, energy minimization) say n times with the energy minimized structure from end of cycle 1 to be used as starting structure for cycle 2. I was wondering is there a way to do this as a loop with just one command line?

Many thanks,

Neena Eappen
Graduate Student
Jockusch Lab<http://www.chem.utoronto.ca/wp/jockusch/>, U of T

From goossens_kenny at hotmail.com  Sun Jan  5 22:26:46 2020
From: goossens_kenny at hotmail.com (Kenny Goossens)
Date: Sun, 05 Jan 2020 21:26:46 -0000
Subject: [gmx-users] Simulated Annealing command line
In-Reply-To: <YT1PR01MB37230F186B52FAD60AD177CFCD3D0@YT1PR01MB3723.CANPRD01.PROD.OUTLOOK.COM>
References: <YT1PR01MB37230F186B52FAD60AD177CFCD3D0@YT1PR01MB3723.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <AM0PR01MB65144B30576AC03C828D240AF83D0@AM0PR01MB6514.eurprd01.prod.exchangelabs.com>

Hi,

For example, if you name your inputfile system1.gro you can use:
for i in {1..n}; do j=$((i + 1));

followed by your grompp and mdrun commands, using ${i} in the names of your input files and ${j} in the names of your output files.

With kind regards,
______________________________
Kenneth Goossens, PhD student
Laboratory of Medicinal Chemistry (Building A - Room 2.13)
University of Antwerp - Campus Drie Eiken
Universiteitsplein 1
B-2610 Wilrijk
Belgium


________________________________
Van: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> namens Neena Susan Eappen <neena.susaneappen at mail.utoronto.ca>
Verzonden: zondag 5 januari 2020 21:43
Aan: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
Onderwerp: [gmx-users] Simulated Annealing command line

Hello gromacs users,

For simulated annealing, I want to repeat cycle (equilibration, annealing, production run, energy minimization) say n times with the energy minimized structure from end of cycle 1 to be used as starting structure for cycle 2. I was wondering is there a way to do this as a loop with just one command line?

Many thanks,

Neena Eappen
Graduate Student
Jockusch Lab<http://www.chem.utoronto.ca/wp/jockusch/>, U of T
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

From dallas.warren at monash.edu  Sun Jan  5 23:00:50 2020
From: dallas.warren at monash.edu (Dallas Warren)
Date: Sun, 05 Jan 2020 22:00:50 -0000
Subject: [gmx-users] molecule breakage during minimization
In-Reply-To: <CACWq+69F+AMqWkDr2XPEpNaU72=KsxNbg3wtLyt1091Ze6V2hw@mail.gmail.com>
References: <CACWq+69F+AMqWkDr2XPEpNaU72=KsxNbg3wtLyt1091Ze6V2hw@mail.gmail.com>
Message-ID: <CAOv1qzb4AiLzN8LDm32Fk3AX7v5WMk-taRavZbQbnphwY+RX2A@mail.gmail.com>

The molecules will not be broken, it is a visualisation artifact.

http://manual.gromacs.org/documentation/2018.5/user-guide/terminology.html#periodic-boundary-conditions

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Fri, 3 Jan 2020 at 07:58, Yogesh Sharma <yogesh.rma13 at gmail.com> wrote:

> Hello everyone,
> Before equillibriation I was trying to minimize my protein membrane system.
> energyminimized.gro file  when vizualized in vmd showed few lipid molecules
> broken. Is it safe to use trjconv to make whole molecule after em or i can
> proceed with breakage? This is the minimization.mdp file I am using
> define                  = -DREST_ON -DSTEP6_0
> integrator              = steep
> emtol                   = 1000.0
> nsteps                  = 5000
> nstlist                 = 10
> cutoff-scheme           = Verlet
> rlist                   = 1.2
> vdwtype                 = Cut-off
> vdw-modifier            = Force-switch
> rvdw_switch             = 1.0
> rvdw                    = 1.2
> coulombtype             = pme
> rcoulomb                = 1.2
> ;
> constraints             = h-bonds
> constraint_algorithm    = LINCS
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From dallas.warren at monash.edu  Sun Jan  5 23:06:07 2020
From: dallas.warren at monash.edu (Dallas Warren)
Date: Sun, 05 Jan 2020 22:06:07 -0000
Subject: [gmx-users] compressibility values in coarse grained simulations
In-Reply-To: <CAB16xbSrgk718ge2r-v6=fjDzivN1cbOjHo9xiHXO=HZQtqgMg@mail.gmail.com>
References: <CAB16xbSrgk718ge2r-v6=fjDzivN1cbOjHo9xiHXO=HZQtqgMg@mail.gmail.com>
Message-ID: <CAOv1qzawhnegOreV1k_h_LhTguU2TzisbFp_w+x1Gv8ZLJckyQ@mail.gmail.com>

http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#mdp-value-pcoupltype=semiisotropic

2 for each.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Fri, 3 Jan 2020 at 22:03, Deepanshi . <tdeepanshi248 at gmail.com> wrote:

> Dear all,
>
> I am using the coarse-grained molecular dynamics simulation to study
> membranes. In the production run .mdp file, to control the pressure I am
> using semiisotropic in the Pcoupltype option. I wanted to ask how many
> values I should give to compressibility and ref_p and what will happen if I
> give more or fewer values than the actual values?
> Also, I wanted to ask that for coarse-grained simulations the value for
> compressibility should be 3e-5 or 4e-5?
>
> Thanks.
>
> Regards,
> Deepanshi.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From 3325574168 at qq.com  Mon Jan  6 09:52:22 2020
From: 3325574168 at qq.com (=?ISO-8859-1?B?MDA4?=)
Date: Mon, 06 Jan 2020 08:52:22 -0000
Subject: [gmx-users] gmx covar error in gromacs2019.x
Message-ID: <tencent_7B8AE85FF3C1E2E682EEC197DDC3CEF56106@qq.com>

Hi gmx users!
I am using gmx2019.4 in centos 7.6 (gcc version 4.8.5), the MD was conducted successfully. However, when I proceeded the PCA analysis, there was a wrong in the output informations.


command:
echo 3 3|gmx covar -f md_res_center_mol_fit_protein.xtc -s ../md.tpr -o eigenvalues.xvg -v eigenvectors.trr -xpma covapic.xpm -n ../index.ndx


output:
Choose a group for the least squares fit
Group&nbsp; &nbsp; &nbsp;0 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;System) has 124748 elements
Group&nbsp; &nbsp; &nbsp;1 (&nbsp; &nbsp; &nbsp; &nbsp; Protein) has&nbsp; 8851 elements
Group&nbsp; &nbsp; &nbsp;2 (&nbsp; &nbsp; &nbsp; Protein-H) has&nbsp; 4419 elements
Group&nbsp; &nbsp; &nbsp;3 (&nbsp; &nbsp; &nbsp; &nbsp; C-alpha) has&nbsp; &nbsp;574 elements
Group&nbsp; &nbsp; &nbsp;4 (&nbsp; &nbsp; &nbsp; &nbsp;Backbone) has&nbsp; 1722 elements
Group&nbsp; &nbsp; &nbsp;5 (&nbsp; &nbsp; &nbsp; MainChain) has&nbsp; 2298 elements
Group&nbsp; &nbsp; &nbsp;6 (&nbsp; &nbsp;MainChain+Cb) has&nbsp; 2824 elements
Group&nbsp; &nbsp; &nbsp;7 (&nbsp; &nbsp; MainChain+H) has&nbsp; 2852 elements
Group&nbsp; &nbsp; &nbsp;8 (&nbsp; &nbsp; &nbsp; SideChain) has&nbsp; 5999 elements
Group&nbsp; &nbsp; &nbsp;9 (&nbsp; &nbsp; SideChain-H) has&nbsp; 2121 elements
Group&nbsp; &nbsp; 10 (&nbsp; &nbsp; Prot-Masses) has&nbsp; 8851 elements
Group&nbsp; &nbsp; 11 (&nbsp; &nbsp; non-Protein) has 115897 elements
Group&nbsp; &nbsp; 12 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Other) has&nbsp; &nbsp; 23 elements
Group&nbsp; &nbsp; 13 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; MOL) has&nbsp; &nbsp; 23 elements
Group&nbsp; &nbsp; 14 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;NA) has&nbsp; &nbsp; &nbsp;8 elements
Group&nbsp; &nbsp; 15 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Water) has 115866 elements
Group&nbsp; &nbsp; 16 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; SOL) has 115866 elements
Group&nbsp; &nbsp; 17 (&nbsp; &nbsp; &nbsp; non-Water) has&nbsp; 8882 elements
Group&nbsp; &nbsp; 18 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Ion) has&nbsp; &nbsp; &nbsp;8 elements
Group&nbsp; &nbsp; 19 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; MOL) has&nbsp; &nbsp; 23 elements
Group&nbsp; &nbsp; 20 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;NA) has&nbsp; &nbsp; &nbsp;8 elements
Group&nbsp; &nbsp; 21 ( Water_and_ions) has 115874 elements
Group&nbsp; &nbsp; 22 (&nbsp; &nbsp; Protein_lig) has&nbsp; 8874 elements
Group&nbsp; &nbsp; 23 (center_Val108_A) has&nbsp; &nbsp; 16 elements
Group&nbsp; &nbsp; 24 (&nbsp; &nbsp; &nbsp; &nbsp; chain_A) has&nbsp; 4427 elements
Group&nbsp; &nbsp; 25 (&nbsp; &nbsp; &nbsp; &nbsp; chain_B) has&nbsp; 4424 elements
Group&nbsp; &nbsp; 26 (C-alpha_&amp;_chain_A) has&nbsp; &nbsp;287 elements
Group&nbsp; &nbsp; 27 (C-alpha_&amp;_chain_B) has&nbsp; &nbsp;287 elements
Group&nbsp; &nbsp; 28 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; E53) has&nbsp; &nbsp; 15 elements
Group&nbsp; &nbsp; 29 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;K135) has&nbsp; &nbsp; 22 elements
Group&nbsp; &nbsp; 30 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;C169) has&nbsp; &nbsp; 11 elements
Group&nbsp; &nbsp; 31 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; S) has&nbsp; &nbsp; &nbsp;1 elements
Group&nbsp; &nbsp; 32 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; C13) has&nbsp; &nbsp; &nbsp;1 elements
Select a group: Selected 3: 'C-alpha'


Choose a group for the covariance analysis
Group&nbsp; &nbsp; &nbsp;0 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;System) has 124748 elements
Group&nbsp; &nbsp; &nbsp;1 (&nbsp; &nbsp; &nbsp; &nbsp; Protein) has&nbsp; 8851 elements
Group&nbsp; &nbsp; &nbsp;2 (&nbsp; &nbsp; &nbsp; Protein-H) has&nbsp; 4419 elements
Group&nbsp; &nbsp; &nbsp;3 (&nbsp; &nbsp; &nbsp; &nbsp; C-alpha) has&nbsp; &nbsp;574 elements
Group&nbsp; &nbsp; &nbsp;4 (&nbsp; &nbsp; &nbsp; &nbsp;Backbone) has&nbsp; 1722 elements
Group&nbsp; &nbsp; &nbsp;5 (&nbsp; &nbsp; &nbsp; MainChain) has&nbsp; 2298 elements
Group&nbsp; &nbsp; &nbsp;6 (&nbsp; &nbsp;MainChain+Cb) has&nbsp; 2824 elements
Group&nbsp; &nbsp; &nbsp;7 (&nbsp; &nbsp; MainChain+H) has&nbsp; 2852 elements
Group&nbsp; &nbsp; &nbsp;8 (&nbsp; &nbsp; &nbsp; SideChain) has&nbsp; 5999 elements
Group&nbsp; &nbsp; &nbsp;9 (&nbsp; &nbsp; SideChain-H) has&nbsp; 2121 elements
Group&nbsp; &nbsp; 10 (&nbsp; &nbsp; Prot-Masses) has&nbsp; 8851 elements
Group&nbsp; &nbsp; 11 (&nbsp; &nbsp; non-Protein) has 115897 elements
Group&nbsp; &nbsp; 12 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Other) has&nbsp; &nbsp; 23 elements
Group&nbsp; &nbsp; 13 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; MOL) has&nbsp; &nbsp; 23 elements
Group&nbsp; &nbsp; 14 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;NA) has&nbsp; &nbsp; &nbsp;8 elements
Group&nbsp; &nbsp; 15 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Water) has 115866 elements
Group&nbsp; &nbsp; 16 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; SOL) has 115866 elements
Group&nbsp; &nbsp; 17 (&nbsp; &nbsp; &nbsp; non-Water) has&nbsp; 8882 elements
Group&nbsp; &nbsp; 18 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Ion) has&nbsp; &nbsp; &nbsp;8 elements
Group&nbsp; &nbsp; 19 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; MOL) has&nbsp; &nbsp; 23 elements
Group&nbsp; &nbsp; 20 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;NA) has&nbsp; &nbsp; &nbsp;8 elements
Group&nbsp; &nbsp; 21 ( Water_and_ions) has 115874 elements
Group&nbsp; &nbsp; 22 (&nbsp; &nbsp; Protein_lig) has&nbsp; 8874 elements
Group&nbsp; &nbsp; 23 (center_Val108_A) has&nbsp; &nbsp; 16 elements
Group&nbsp; &nbsp; 24 (&nbsp; &nbsp; &nbsp; &nbsp; chain_A) has&nbsp; 4427 elements
Group&nbsp; &nbsp; 25 (&nbsp; &nbsp; &nbsp; &nbsp; chain_B) has&nbsp; 4424 elements
Group&nbsp; &nbsp; 26 (C-alpha_&amp;_chain_A) has&nbsp; &nbsp;287 elements
Group&nbsp; &nbsp; 27 (C-alpha_&amp;_chain_B) has&nbsp; &nbsp;287 elements
Group&nbsp; &nbsp; 28 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; E53) has&nbsp; &nbsp; 15 elements
Group&nbsp; &nbsp; 29 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;K135) has&nbsp; &nbsp; 22 elements
Group&nbsp; &nbsp; 30 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;C169) has&nbsp; &nbsp; 11 elements
Group&nbsp; &nbsp; 31 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; S) has&nbsp; &nbsp; &nbsp;1 elements
Group&nbsp; &nbsp; 32 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; C13) has&nbsp; &nbsp; &nbsp;1 elements
Select a group: Selected 3: 'C-alpha'
Calculating the average structure ...
Reading frame&nbsp; &nbsp; &nbsp; &nbsp;0 time&nbsp; &nbsp; 0.000&nbsp; &nbsp;
WARNING: number of atoms in tpx (574) and trajectory (8851) do not match
Last frame&nbsp; &nbsp; &nbsp; 10000 time&nbsp;100000.000&nbsp; &nbsp;


Back Off! I just backed up average.pdb to ./#average.pdb.3#
Constructing covariance matrix (1722x1722) ...
Last frame&nbsp; &nbsp; &nbsp; 10000 time&nbsp;100000.000&nbsp; &nbsp;
Read 10001 frames


Trace of the covariance matrix: 9.58344 (nm^2)


Back Off! I just backed up covapic.xpm to ./#covapic.xpm.3#
100%
Diagonalizing ...


-------------------------------------------------------
Program:&nbsp; &nbsp; &nbsp;gmx covar, version 2019.4
Source file: src/gromacs/linearalgebra/eigensolver.cpp (line 137)


Fatal error:
Internal errror in LAPACK diagonalization.


For more information and tips for troubleshooting, please check the GROMACS
website at&nbsp;http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------




I had tested the same files in a virtual machine with centos 7.6 and gmx2019.4 installed, the output was normal and gave the output files I need. Then I used the same files on other server with gmx 4.5.3, and the md.tpr was replaced by md.gro, it was also normal. I had installed gmx2019.2, gmx2019.5 and it gave the same error.


the gmx was installed as follows:


cmake(version 3.16.0)

tar xvf cmake-*.tar.gz &amp;&amp; cd cmake-*
./bootstrap
gmake &amp;&amp; gmake install
yum remove cmake -y
ln -s /usr/local/bin/cmake /usr/bin/


fftw-3.3.8
tar -zxvf fftw* &amp;&amp; cd fftw*
./configure --prefix=/usr/local/fftw3.3.8 --enable-sse2 --enable-avx&nbsp; --enable-avx2 --enable-float --enable-shared
make install -j 16


gmx2019.4
&nbsp; &nbsp; tar xfz gromacs-2019.4.tar.gz &amp;&amp; cd gromacs-2019.4
&nbsp; &nbsp; mkdir build &amp;&amp; cd build
&nbsp; &nbsp; export CMAKE_PREFIX_PATH=/usr/local/fftw3.3.8

&nbsp; &nbsp; cmake .. -DCMAKE_INSTALL_PREFIX=/opt/software/gmx2019.4 -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-10.2
&nbsp; &nbsp; make -j 16
&nbsp; &nbsp; make check
&nbsp; &nbsp; make install




Thanks in advance.
Regards

From deligkaris at gmail.com  Mon Jan  6 20:59:58 2020
From: deligkaris at gmail.com (Christos Deligkaris)
Date: Mon, 06 Jan 2020 19:59:58 -0000
Subject: [gmx-users] atom moved too far
In-Reply-To: <edcb7673-b113-dcc4-810d-125ef89842f5@vt.edu>
References: <CAAHQ3wnYn0XapewAPd0RoAsC0HZLVJ_CjYU5bZOtDPd=u8aw4g@mail.gmail.com>
	<eb6b4386-8d1c-0a69-d59b-bde928a48d87@vt.edu>
	<CAAHQ3wmpoDWc1BNT90XsEARLe9gV=AVCCejonzouFvOtXqefeA@mail.gmail.com>
	<edcb7673-b113-dcc4-810d-125ef89842f5@vt.edu>
Message-ID: <CAAHQ3wmURZ_x2RCP-pcasra94BOpAZQNtR86xcCSxF88pVjYKQ@mail.gmail.com>

Justin, thank you.

I have implemented the pull code but that also exhibits the same error when
I use 12 cores (failed at about 2ns) and the simulation goes on fine when I
use 6 cores (now at about 32 ns).

I tried using the v-rescale thermostat (instead of Nose-Hoover) and
Parinello-Rahman barostat, which failed. I also tried the v-rescale
thermostat and the Berendsen barostat but that also failed. It seems to me
that this is not an equilibration issue.

So, to summarize, only if I decrease the time step to 0.001 ps or decrease
the number of cores seem to allow the calculation to proceed.

In this email list, I read that someone else was trying to use different
arguments supplied to mdrun (-nt, -ntomp etc) to solve the same problem. Is
it possible that the problem arises due to my running gmx_mpi on a single
node? This is the command I use in my submission script:

mpirun --mca btl tcp,sm,self /opt/gromacs-2018.1/bin/gmx_mpi mdrun -ntomp
\$ntomp -v -deffnm "${inputfile%.tpr}"

If you think that this is not due to a physics issue I can continue doing
calculations with 6 cores and try to install gromacs 2020 (both gmx and
gmx_mpi) to see if my problem persists there or not...


Best wishes,

Christos Deligkaris, PhD


On Thu, Jan 2, 2020 at 7:48 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/2/20 3:02 PM, Christos Deligkaris wrote:
> > thank you Justin.
> >
> > I saw on your umbrella sampling tutorial how to implement the restraints
> > using the pull code.
> >
> > The protocol I used is (if I understand correctly your question): The
> > energy minimization reached the cutoff for maximum force 1000 in 346
> steps.
> > My NVT equilibration was 50,000 steps of dt = 0.002 and I used 8 NPT
> > equilibration calculations, each with 31,250 steps of dt=0.002 (total NPT
> > equilibration time 500ps) where I slowly decreased the position
> restraints
> > on DNA and the small molecule, as well as the harmonic restraint between
> > the two.
> > What are the best temperature coupling groups to use when we are not
> > certain whether the small molecule will spend the entire simulation
> period
> > physically bound to the macromolecule or whether it will become fully
> > solvated at some point? Is Macromolecule and Non-macromolecule the best
> > option since the small molecule will always (to a small or large extent)
> > interact with water (versus the Macromolecule_and_small_molecule and
> > everything else grouping option)?
>
> I doubt there would be a measurable or provable difference between the
> behaviors of the two setups.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From marcelodepolo at gmail.com  Mon Jan  6 22:47:04 2020
From: marcelodepolo at gmail.com (=?UTF-8?Q?Marcelo_Dep=C3=B3lo?=)
Date: Mon, 06 Jan 2020 21:47:04 -0000
Subject: [gmx-users] CMAP format on GROMCACS
Message-ID: <CAFAAhpYQrO91e6NXDgz_-aV5B-OpQjwzqGR=EV3FPDS_MqYfwQ@mail.gmail.com>

Hi everybody! Happy new year! =)


I would like to understand a little bit better the CMAP format of
charmm27.ff within GROMACS. I've looked up in the manual but found little
information.

I understand that it is defined by 5 atoms (1-4 phi and 2-5 psi), a
arbitrary identification number (e.g. 1) and the grid size (e.g. 24x24).
But the following grid values are lines with just 10 values each, ended
with a "\", instead of a 24 columns- 24 lines matrix.

How are those values of CMAP formatted  in GMX? Does GMX automatically
transform those values in a matrix and, if so, can I consider that its
"y-axis" would be PSI and "x-axis" would be PHI?

Cheers!
--
Marcelo Dep?lo Pol?to
Postdoctoral Researcher
BIOAGRO - Room T07
Department of General Biology - UFV
Contact: + 55 31 3612-2464

From roland.schulz at intel.com  Tue Jan  7 02:22:20 2020
From: roland.schulz at intel.com (Schulz, Roland)
Date: Tue, 07 Jan 2020 01:22:20 -0000
Subject: [gmx-users] Need help with installation of Gromacs-2019.3 with
 Intell compilers
In-Reply-To: <CABJycMD1HkqOTvgikfsesRf+H+9Oo8cPWXU4E_0eUUNBY0iLiQ@mail.gmail.com>
References: <CADg3LA+Z449EhxF82Yf_0XUt7rxqk9U288ZP2mEPLFxV9ENXWg@mail.gmail.com>
	<a36f69e8-f8ac-83e1-5040-a28cd0673559@gmail.com>
	<CADg3LA+tupwUUqTn95cDuSS0x4hOXWB7+exctu5K1_1r_nZz5A@mail.gmail.com>
	<CABJycMD1HkqOTvgikfsesRf+H+9Oo8cPWXU4E_0eUUNBY0iLiQ@mail.gmail.com>
Message-ID: <BYAPR11MB2581F3EEC9AA5311ED0FB0ABE03F0@BYAPR11MB2581.namprd11.prod.outlook.com>

Hi,

As a work-around it is possible to put "#pragma intel optimization_level 2" in front pull_calc_coms in file src/gromacs/pulling/pullutil.cpp or use Intel compiler 2019u4 which doesn't have the problem.
Lowering the optimization for the one function shouldn't have a significant impact on performance even if you use pulling because this function isn't compute intensive. A full fix is in the works.

Roland

> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of Rajib
> Biswas
> Sent: Monday, December 30, 2019 6:13 AM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Need help with installation of Gromacs-2019.3 with
> Intell compilers
> 
> Dear Gromacs-Users,
> 
> Is there any update on this issue? I have used the following flags for version
> 2019.3
> 
> /apps/codes/cmake/3.15.4/bin/cmake ..
> -DCMAKE_INSTALL_PREFIX=/opt/gromacs/2019.3 -
> DGMX_FFT_LIBRARY=fftw3
> -DCMAKE_PREFIX_PATH=/apps/libs/fftw/3.3.8 -DBUILD_SHARED_LIBS=OFF
> -DGMX_DOUBLE=ON -DGMX_SIMD=AVX2_256 -
> DCMAKE_C_COMPILER=mpiicc -DCMAKE_CXX_COMPILER=mpiicpc -
> DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_BUILD_MDRUN_ONLY=ON
> 
> and getting compilation error which says:
> 
> [ 58%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o
> icpc: error #10105:
> /apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom:
> core dumped
> icpc: warning #10102: unknown signal(-497903120)
> icpc: error #10106: Fatal error in
> /apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom,
> terminated by unknown
> compilation aborted for
> /storage/rajib/opt/gromacs-2019.3/src/gromacs/pulling/pullutil.cpp (code 1)
> make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o]
> Error 1
> make[2]: *** Waiting for unfinished jobs....
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> make: *** [all] Error 2
> 
> Your help will be highly appreciated.
> 
> Thanking you.
> 
> With regards,
> Rajib
> 
> 
> 
> On Wed, Oct 9, 2019 at 4:03 AM Lyudmyla Dorosh <dorosh at ualberta.ca>
> wrote:
> 
> > I have tried this command line:
> > sudo cmake .. -DBUILD_SHARED_LIBS=OFF -DGMX_FFT_LIBRARY=mkl
> > -DCMAKE_INSTALL_PREFIX=$installDir -DGMX_MPI=ON -
> DGMX_OPENMP=ON
> > -DGMX_CYCLE_SUBCOUNTERS=ON -DGMX_GPU=OFF -DGMX_SIMD=SSE2
> > -DCMAKE_C_COMPILER="/home/doroshl/apps/intel/bin/icc"
> > -DCMAKE_CXX_COMPILER="/home/doroshl/apps/intel/bin/icpc"
> > -DREGRESSIONTEST_DOWNLOAD=ON
> > which had no errors for *cmake* or *make -j 4*, but *make check* gave
> > me an
> > error:
> > ...
> > [100%] Running all tests except physical validation Test project
> > /home/doroshl/gromacs-2019.3/build
> >       Start  1: TestUtilsUnitTests
> >  1/46 Test  #1: TestUtilsUnitTests ..................***Failed    0.00 sec
> > /home/doroshl/gromacs-2019.3/build/bin/testutils-test: error while
> > loading shared libraries: libmkl_intel_lp64.so: cannot open shared
> > object file: No such file or directory ...
> > 0% tests passed, 46 tests failed out of 46
> >
> > so I included libmkl_intel_lp64.so:
> > sudo cmake .. -DBUILD_SHARED_LIBS=OFF -DGMX_FFT_LIBRARY=mkl
> > -DCMAKE_INSTALL_PREFIX=$installDir
> >
> > -
> DMKL_LIBRARIES="/home/doroshl/apps/intel/compilers_and_libraries_2019
> .5.281/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so"
> > -DMKL_INCLUDE_DIR="/home/doroshl/apps/intel/intelpython2/lib"
> > -DCMAKE_CXX_LINK_FLAGS="-Wl,-rpath,/usr/bin/gcc/lib64 -
> L/usr/bin/gcc/lib64"
> > -DGMX_MPI=ON -DGMX_OPENMP=ON -
> DGMX_CYCLE_SUBCOUNTERS=ON -DGMX_GPU=OFF
> > -DGMX_SIMD=SSE2 -
> DCMAKE_C_COMPILER="/home/doroshl/apps/intel/bin/icc"
> > -DCMAKE_CXX_COMPILER="/home/doroshl/apps/intel/bin/icpc"
> > -DREGRESSIONTEST_DOWNLOAD=ON &> cmake.out which doesn't give
> any error
> > messages for cmake, but then in *sudo make -j
> > 4 *results in
> >
> > [ 46%] Building CXX object
> > src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o
> > icpc: error #10105:
> >
> >
> /home/doroshl/apps/intel/compilers_and_libraries_2019.5.281/linux/bin/int
> el64/mcpcom:
> > core dumped
> > icpc: warning #10102: unknown signal(694380720)
> > icpc: error #10106: Fatal error in
> >
> > /home/doroshl/apps/intel/compilers_and_libraries_2019.5.281/linux/bin/
> > intel64/mcpcom,
> > terminated by unknown
> > compilation aborted for
> > /home/doroshl/gromacs-2019.3/src/gromacs/pulling/pullutil.cpp (code 1)
> > src/gromacs/CMakeFiles/libgromacs.dir/build.make:2136: recipe for
> > target 'src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o'
> > failed
> > make[2]: ***
> > [src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o]
> > Error 1
> > make[2]: *** Waiting for unfinished jobs....
> > CMakeFiles/Makefile2:2499: recipe for target
> > 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
> > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> > Makefile:162: recipe for target 'all' failed
> > make: *** [all] Error 2
> > Thanks for any help
> >
> >
> > On Tue, Oct 8, 2019 at 2:21 AM Paul bauer <paul.bauer.q at gmail.com>
> wrote:
> >
> > > Hej,
> > >
> > > I can't access the repository, so I can't say for certain what happened.
> > > Can you share your cmake command line?
> > >
> > > Cheers
> > >
> > > Paul
> > >
> > > On 07/10/2019 21:25, Lyudmyla Dorosh wrote:
> > > > Hello Gromacs Developers/Users,
> > > >
> > > > I'm trying to install Gromacs-2019.3 on Intel Xeon W-2175 with
> > > > Intel compilers (+MKL+MPI).
> > > > First I compiled cmake with Intel compilers. All output files are
> > > attached.
> > > > cmake, make seemed to go ok, but all check test failed. What do I
> > > > do
> > > wrong?
> > > >
> > >
> >
> https://drive.google.com/file/d/1M8aOaq7ocmK4UOAzcRb5AqWMihIhVtmn
> /view
> > ?usp=sharing
> > > >
> > > > Thank you,
> > > >
> > > > Lyudmyla Dorosh, PhD
> > > > ------------------------------------------------------------
> > > > University of Alberta
> > > > Department of Electrical and Computer Engineering,
> > > > 4-021 ECERF
> > > > Edmonton, AB, T6G 2G8
> > > > Canada
> > > > Email: dorosh at ualberta.ca
> > > >
> > >
> > > --
> > > Paul Bauer, PhD
> > > GROMACS Release Manager
> > > KTH Stockholm, SciLifeLab
> > > 0046737308594
> > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > > or send a mail to gmx-users-request at gromacs.org.
> > >
> >
> >
> > --
> > Regards,
> >
> > Lyudmyla Dorosh, PhD
> > ------------------------------------------------------------
> > University of Alberta
> > Department of Electrical and Computer Engineering,
> > 4-021 ECERF
> > Edmonton, AB, T6G 2G8
> > Canada
> > Email: dorosh at ualberta.ca
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
> 
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
> a mail to gmx-users-request at gromacs.org.

From jalemkul at vt.edu  Tue Jan  7 03:29:12 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Tue, 07 Jan 2020 02:29:12 -0000
Subject: [gmx-users] [gmx-user] Autodock Vina Out use in gromacs MD
In-Reply-To: <CAG0e8MP5V6ts7TJMf3ZjT=tH5gHcyxjymE0iqVPqOafg3LJC7A@mail.gmail.com>
References: <CAG0e8MMkVer9b8NEvQoduajr3ggFVkXJW6_C-L+9cqB-SimUJQ@mail.gmail.com>
	<CAG0e8MM+Ep=ptOhmCN4XKymbmBXcCQV6GcvE-CsmTvgY8NwdoA@mail.gmail.com>
	<921bd165-2e24-4e27-9664-b2f5bd382f72@vt.edu>
	<CAG0e8MP5V6ts7TJMf3ZjT=tH5gHcyxjymE0iqVPqOafg3LJC7A@mail.gmail.com>
Message-ID: <d77121e1-3be5-8b05-57f7-56220de5a450@vt.edu>



On 1/4/20 1:17 PM, Quin K wrote:
> Dear Proffesor Lemkul,
>
> I have given below the MD RMSD for complex, and noted that Ligand is
> getting detached again. When I viewed the trajectory on VMD it was
> confirmed.  The ligand did not abruptly got dislodged instead it slowly
> came out of binding pocket and started moving around after.
> https://drive.google.com/file/d/1IBMU-8SzSgXVr_h9zyeVwNV7kQ4at8-S/view?usp=sharing

It would be more useful to investigate which interactions are broken 
first or if there is a dihedral that rotates that leads to a 
conformational change in the ligand. RMSD tells you very little.

> I know that following CGenFF tutorial and fixing the molecule and
> reparameterization would be the correct thing to do however I lack time at
> this moment.
> I read the paper and went through the tutorial and it's some what of a
> complex method to fix the parameters.
> I was thinking if I should use a different force-field such as Gromos with
> parameterization with ATB server.
> I have already submitted the given molecule below for optimization in ATB
> and the parameterization is now complete.
> Other option is to use Amber force field. Kindly let me know what your
> opinion on this.

The nice thing about CGenFF is it tells you where it thinks problems 
might be and how they score in terms of quality. Neither of the other 
options do that. You always need to validate a ligand topology. Black 
boxes might work well or they might work poorly. You just don't know.

> Molecule
> https://drive.google.com/file/d/1Ni8rUX4sH3aKaRhhXqCZr9w8VJVetCI7/view?usp=sharing
>
> Interactions at binding site us DS Visualizer
> https://drive.google.com/file/d/16EkWYDPDyTfkERiQgaOYo4XxYxqslOD0/view?usp=sharing
>
> Also please let me know if you think the given interactions are enough to
> keep the molecule at binding site for like 100ns?

The Arg-ligand interaction should be pretty strong, but you have an 
identified "unfavorable" contact (which could be due to the rotameric 
state of Asn111 being suboptimal, and otherwise only nonpolar contacts. 
I wouldn't expect a very favorable binding free energy.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From jalemkul at vt.edu  Tue Jan  7 03:30:04 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Tue, 07 Jan 2020 02:30:04 -0000
Subject: [gmx-users] atom moved too far
In-Reply-To: <CAAHQ3wmURZ_x2RCP-pcasra94BOpAZQNtR86xcCSxF88pVjYKQ@mail.gmail.com>
References: <CAAHQ3wnYn0XapewAPd0RoAsC0HZLVJ_CjYU5bZOtDPd=u8aw4g@mail.gmail.com>
	<eb6b4386-8d1c-0a69-d59b-bde928a48d87@vt.edu>
	<CAAHQ3wmpoDWc1BNT90XsEARLe9gV=AVCCejonzouFvOtXqefeA@mail.gmail.com>
	<edcb7673-b113-dcc4-810d-125ef89842f5@vt.edu>
	<CAAHQ3wmURZ_x2RCP-pcasra94BOpAZQNtR86xcCSxF88pVjYKQ@mail.gmail.com>
Message-ID: <c845c547-8063-edc6-8e9e-6759be70e35f@vt.edu>



On 1/6/20 2:59 PM, Christos Deligkaris wrote:
> Justin, thank you.
>
> I have implemented the pull code but that also exhibits the same error when
> I use 12 cores (failed at about 2ns) and the simulation goes on fine when I
> use 6 cores (now at about 32 ns).
>
> I tried using the v-rescale thermostat (instead of Nose-Hoover) and
> Parinello-Rahman barostat, which failed. I also tried the v-rescale
> thermostat and the Berendsen barostat but that also failed. It seems to me
> that this is not an equilibration issue.
>
> So, to summarize, only if I decrease the time step to 0.001 ps or decrease
> the number of cores seem to allow the calculation to proceed.
>
> In this email list, I read that someone else was trying to use different
> arguments supplied to mdrun (-nt, -ntomp etc) to solve the same problem. Is
> it possible that the problem arises due to my running gmx_mpi on a single
> node? This is the command I use in my submission script:
>
> mpirun --mca btl tcp,sm,self /opt/gromacs-2018.1/bin/gmx_mpi mdrun -ntomp
> \$ntomp -v -deffnm "${inputfile%.tpr}"
>
> If you think that this is not due to a physics issue I can continue doing
> calculations with 6 cores and try to install gromacs 2020 (both gmx and
> gmx_mpi) to see if my problem persists there or not...

If you're running on a single node, there's no need for an external MPI 
library. Perhaps you've got a buggy implementation? Have you tried using 
12 cores via the built-in thread MPI library?

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From jalemkul at vt.edu  Tue Jan  7 03:31:47 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Tue, 07 Jan 2020 02:31:47 -0000
Subject: [gmx-users] CMAP format on GROMCACS
In-Reply-To: <CAFAAhpYQrO91e6NXDgz_-aV5B-OpQjwzqGR=EV3FPDS_MqYfwQ@mail.gmail.com>
References: <CAFAAhpYQrO91e6NXDgz_-aV5B-OpQjwzqGR=EV3FPDS_MqYfwQ@mail.gmail.com>
Message-ID: <4b6ca52e-3b3b-bc31-6458-d206a245332c@vt.edu>



On 1/6/20 4:46 PM, Marcelo Dep?lo wrote:
> Hi everybody! Happy new year! =)
>
>
> I would like to understand a little bit better the CMAP format of
> charmm27.ff within GROMACS. I've looked up in the manual but found little
> information.
>
> I understand that it is defined by 5 atoms (1-4 phi and 2-5 psi), a
> arbitrary identification number (e.g. 1) and the grid size (e.g. 24x24).
> But the following grid values are lines with just 10 values each, ended
> with a "\", instead of a 24 columns- 24 lines matrix.
>
> How are those values of CMAP formatted  in GMX? Does GMX automatically
> transform those values in a matrix and, if so, can I consider that its
> "y-axis" would be PSI and "x-axis" would be PHI?

The \ are line continuation characters, so GROMACS is reading a 24x24 
matrix in a single array of values.

The values are written for all values of phi at a given value of psi, 
i.e. writing each row of the matrix, starting from phi = -180, psi = 
-180 until phi = 180, psi = 180.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From byunjy0614 at gmail.com  Tue Jan  7 03:38:54 2020
From: byunjy0614 at gmail.com (=?utf-8?B?67OA7KeE7JiB?=)
Date: Tue, 07 Jan 2020 02:38:54 -0000
Subject: [gmx-users] The maxwarn fatal errors
In-Reply-To: <50208.160.45.109.123.1576061007.webmail@webmail.zedat.fu-berlin.de>
References: <8451E109-80A6-4EA4-99DD-BAA53FB29616@gmail.com>
	<6951b957-497a-5694-bba5-ed409a063673@vt.edu>
	<50208.160.45.109.123.1576061007.webmail@webmail.zedat.fu-berlin.de>
Message-ID: <4B64C77F-360F-44CA-B051-11DF14D7F2C7@gmail.com>

Dear everyone, Happy New year!
I have gone through the Justin Lemku tutorial for Umbrella Sampling. During tutorial, When I treid to input the command line:
  gmx grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -r npt0.gro -n index.ndx -o umbrella0.tpr

I have met two warnings and they occured fatal error.:
  Fatal error:
  Too many warnings (2).
   If you are sure all warnings are harmless, use the -maxwarn option.

And the waring is:
 WARNING 1 [file topol.top, line 56]:
  The GROMOS force fields have been parametrized with a physically
  incorrect multiple-time-stepping scheme for a twin-range cut-off. When
  used with a single-range cut-off (or a correct Trotter
  multiple-time-stepping scheme), physical properties, such as the density,
  might differ from the intended values. Since there are researchers
  actively working on validating GROMOS with modern integrators we have not
  yet removed the GROMOS force fields, but you should be aware of these
  issues and check if molecules in your system are affected before
  proceeding. Further information is available at
  https://redmine.gromacs.org/issues/2884 , and a longer explanation of our
  decision to remove physically incorrect algorithms can be found at
  https://doi.org/10.26434/chemrxiv.11474583.v1 .


WARNING 2 [file md_umbrella.mdp]:
  With Nose-Hoover T-coupling and Parrinello-Rahman p-coupling, tau-p (1)
  should be at least twice as large as tau-t (1) to avoid resonances

I solved this problem with using -maxwarn option but I am wondering whether thses warning is passed over.
What do you think what I happend? dears. Any idea on what caused this problem?

From jalemkul at vt.edu  Tue Jan  7 03:41:39 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Tue, 07 Jan 2020 02:41:39 -0000
Subject: [gmx-users] The maxwarn fatal errors
In-Reply-To: <4B64C77F-360F-44CA-B051-11DF14D7F2C7@gmail.com>
References: <8451E109-80A6-4EA4-99DD-BAA53FB29616@gmail.com>
	<6951b957-497a-5694-bba5-ed409a063673@vt.edu>
	<50208.160.45.109.123.1576061007.webmail@webmail.zedat.fu-berlin.de>
	<4B64C77F-360F-44CA-B051-11DF14D7F2C7@gmail.com>
Message-ID: <89785204-b49e-4f0c-3da9-10abd0b13d1c@vt.edu>



On 1/6/20 9:40 PM, ??? wrote:
> Dear everyone, Happy New year!
> I have gone through the Justin Lemku tutorial for Umbrella Sampling. During tutorial, When I treid to input the command line:
>    gmx grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -r npt0.gro -n index.ndx -o umbrella0.tpr
>
> I have met two warnings and they occured fatal error.:
>    Fatal error:
>    Too many warnings (2).
>     If you are sure all warnings are harmless, use the -maxwarn option.
>
> And the waring is:
>   WARNING 1 [file topol.top, line 56]:
>    The GROMOS force fields have been parametrized with a physically
>    incorrect multiple-time-stepping scheme for a twin-range cut-off. When
>    used with a single-range cut-off (or a correct Trotter
>    multiple-time-stepping scheme), physical properties, such as the density,
>    might differ from the intended values. Since there are researchers
>    actively working on validating GROMOS with modern integrators we have not
>    yet removed the GROMOS force fields, but you should be aware of these
>    issues and check if molecules in your system are affected before
>    proceeding. Further information is available at
>    https://redmine.gromacs.org/issues/2884 , and a longer explanation of our
>    decision to remove physically incorrect algorithms can be found at
>    https://doi.org/10.26434/chemrxiv.11474583.v1 .
>
>
> WARNING 2 [file md_umbrella.mdp]:
>    With Nose-Hoover T-coupling and Parrinello-Rahman p-coupling, tau-p (1)
>    should be at least twice as large as tau-t (1) to avoid resonances
>
> I solved this problem with using -maxwarn option but I am wondering whether thses warning is passed over.
> What do you think what I happend? dears. Any idea on what caused this problem?

The first warning is very verbose and provides you with substantial 
justification and background reading.

As for the second, change tau-p to 2 as suggested. Note that I have not 
made any attempt to update the tutorials for the 2020 version, and they 
are only guaranteed to be compatible with GROMACS 2018.x versions.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From mark.j.abraham at gmail.com  Tue Jan  7 09:18:44 2020
From: mark.j.abraham at gmail.com (Mark Abraham)
Date: Tue, 07 Jan 2020 08:18:44 -0000
Subject: [gmx-users] The maxwarn fatal errors
In-Reply-To: <4B64C77F-360F-44CA-B051-11DF14D7F2C7@gmail.com>
References: <8451E109-80A6-4EA4-99DD-BAA53FB29616@gmail.com>
	<6951b957-497a-5694-bba5-ed409a063673@vt.edu>
	<50208.160.45.109.123.1576061007.webmail@webmail.zedat.fu-berlin.de>
	<4B64C77F-360F-44CA-B051-11DF14D7F2C7@gmail.com>
Message-ID: <CAMNuMAQk3-tXWbv9PbUadMByzDMicPYZ2+M4nCHu2hKmhS50=A@mail.gmail.com>

Hi,

Warnings mean your physics is probably broken, unless you can explain why
it isn't. Suggestions for fixing them are in the warnings.

Mark

On Tue., 7 Jan. 2020, 03:39 ???, <byunjy0614 at gmail.com> wrote:

> Dear everyone, Happy New year!
> I have gone through the Justin Lemku tutorial for Umbrella Sampling.
> During tutorial, When I treid to input the command line:
>   gmx grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -r
> npt0.gro -n index.ndx -o umbrella0.tpr
>
> I have met two warnings and they occured fatal error.:
>   Fatal error:
>   Too many warnings (2).
>    If you are sure all warnings are harmless, use the -maxwarn option.
>
> And the waring is:
>  WARNING 1 [file topol.top, line 56]:
>   The GROMOS force fields have been parametrized with a physically
>   incorrect multiple-time-stepping scheme for a twin-range cut-off. When
>   used with a single-range cut-off (or a correct Trotter
>   multiple-time-stepping scheme), physical properties, such as the density,
>   might differ from the intended values. Since there are researchers
>   actively working on validating GROMOS with modern integrators we have not
>   yet removed the GROMOS force fields, but you should be aware of these
>   issues and check if molecules in your system are affected before
>   proceeding. Further information is available at
>   https://redmine.gromacs.org/issues/2884 , and a longer explanation of
> our
>   decision to remove physically incorrect algorithms can be found at
>   https://doi.org/10.26434/chemrxiv.11474583.v1 .
>
>
> WARNING 2 [file md_umbrella.mdp]:
>   With Nose-Hoover T-coupling and Parrinello-Rahman p-coupling, tau-p (1)
>   should be at least twice as large as tau-t (1) to avoid resonances
>
> I solved this problem with using -maxwarn option but I am wondering
> whether thses warning is passed over.
> What do you think what I happend? dears. Any idea on what caused this
> problem?
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From neena.susaneappen at mail.utoronto.ca  Tue Jan  7 14:57:11 2020
From: neena.susaneappen at mail.utoronto.ca (Neena Susan Eappen)
Date: Tue, 07 Jan 2020 13:57:11 -0000
Subject: [gmx-users] Simulated Annealing command line
In-Reply-To: <YT1PR01MB37230F186B52FAD60AD177CFCD3D0@YT1PR01MB3723.CANPRD01.PROD.OUTLOOK.COM>
References: <YT1PR01MB37230F186B52FAD60AD177CFCD3D0@YT1PR01MB3723.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <YT1PR01MB37230B3C02ADDF7983A0B987CD3F0@YT1PR01MB3723.CANPRD01.PROD.OUTLOOK.COM>

Hi Kenny,

Thank you for your answer, but I did not understand clearly. For say 30 cycles of simulated annealing, what I have been doing currently is going through the following steps ( equilibration, annealing, production run, energy minimization) 30 times by changing names of input and output files every cycle.
My question is say after the 1st cycle, is there a way to input a single command line to repeat this process say the remaining 29 times by using energy minimized structure from the end of every cycle as the starting structure for the next cycle.

Any insight would be appreciated,

Thank you,

Neena Eappen
Graduate Student
Jockusch Lab<http://www.chem.utoronto.ca/wp/jockusch/>, U of T
________________________________
From: Neena Susan Eappen
Sent: Sunday, January 5, 2020 8:43 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] Simulated Annealing command line

Hello gromacs users,

For simulated annealing, I want to repeat cycle (equilibration, annealing, production run, energy minimization) say n times with the energy minimized structure from end of cycle 1 to be used as starting structure for cycle 2. I was wondering is there a way to do this as a loop with just one command line?

Many thanks,

Neena Eappen
Graduate Student
Jockusch Lab<http://www.chem.utoronto.ca/wp/jockusch/>, U of T

From jalemkul at vt.edu  Tue Jan  7 15:02:14 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Tue, 07 Jan 2020 14:02:14 -0000
Subject: [gmx-users] Simulated Annealing command line
In-Reply-To: <YT1PR01MB37230B3C02ADDF7983A0B987CD3F0@YT1PR01MB3723.CANPRD01.PROD.OUTLOOK.COM>
References: <YT1PR01MB37230F186B52FAD60AD177CFCD3D0@YT1PR01MB3723.CANPRD01.PROD.OUTLOOK.COM>
	<YT1PR01MB37230B3C02ADDF7983A0B987CD3F0@YT1PR01MB3723.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <9720bf5c-9b50-2141-92c8-a480082df4d8@vt.edu>



On 1/7/20 8:57 AM, Neena Susan Eappen wrote:
> Hi Kenny,
>
> Thank you for your answer, but I did not understand clearly. For say 30 cycles of simulated annealing, what I have been doing currently is going through the following steps ( equilibration, annealing, production run, energy minimization) 30 times by changing names of input and output files every cycle.
> My question is say after the 1st cycle, is there a way to input a single command line to repeat this process say the remaining 29 times by using energy minimized structure from the end of every cycle as the starting structure for the next cycle.

It's not a "single command" per se, but it's easy to do this in a 
for-loop in a shell script. As Kenny pointed out, you have two counters, 
i and j, which specify the index of the file to be used. If j=i+1, then 
for cycle $j, you use the coordinates, checkpoint, etc. of cycle $i as 
input to grompp, and then execute mdrun.

-Justin

> Any insight would be appreciated,
>
> Thank you,
>
> Neena Eappen
> Graduate Student
> Jockusch Lab<http://www.chem.utoronto.ca/wp/jockusch/>, U of T
> ________________________________
> From: Neena Susan Eappen
> Sent: Sunday, January 5, 2020 8:43 PM
> To: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] Simulated Annealing command line
>
> Hello gromacs users,
>
> For simulated annealing, I want to repeat cycle (equilibration, annealing, production run, energy minimization) say n times with the energy minimized structure from end of cycle 1 to be used as starting structure for cycle 2. I was wondering is there a way to do this as a loop with just one command line?
>
> Many thanks,
>
> Neena Eappen
> Graduate Student
> Jockusch Lab<http://www.chem.utoronto.ca/wp/jockusch/>, U of T

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From shanjayasinghe2011 at gmail.com  Tue Jan  7 23:39:00 2020
From: shanjayasinghe2011 at gmail.com (Shan Jayasinghe)
Date: Tue, 07 Jan 2020 22:39:00 -0000
Subject: [gmx-users] Make index command in gromacs
Message-ID: <CAChmq0iqZVt=d0eYaQ6xERamDAds4_ZXtdnW=ks2b_zqNKYt3g@mail.gmail.com>

Dear Gromacs Users,

In my simulations, I have different sizes of water droplets.  I need
indexes of water molecules in each droplet separately. I am trying to make
the  index file with gmx make_ndx, but I couldn't do it. Appreciate your
help regarding this matter.

Thank you.
-- 
Best Regards
Shan Jayasinghe

From neena.susaneappen at mail.utoronto.ca  Wed Jan  8 00:35:53 2020
From: neena.susaneappen at mail.utoronto.ca (Neena Susan Eappen)
Date: Tue, 07 Jan 2020 23:35:53 -0000
Subject: [gmx-users] Simulated Annealing command line
In-Reply-To: <YT1PR01MB37230B3C02ADDF7983A0B987CD3F0@YT1PR01MB3723.CANPRD01.PROD.OUTLOOK.COM>
References: <YT1PR01MB37230F186B52FAD60AD177CFCD3D0@YT1PR01MB3723.CANPRD01.PROD.OUTLOOK.COM>,
	<YT1PR01MB37230B3C02ADDF7983A0B987CD3F0@YT1PR01MB3723.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <YT1PR01MB3723D901A5AB97D9AE3A9856CD3F0@YT1PR01MB3723.CANPRD01.PROD.OUTLOOK.COM>

Hi Justin,

Thank you for your answer. I haven't written scripts before, so I was wondering is there a sample script I can see for looping in gromacs.

Thanks,
Neena
________________________________
From: Neena Susan Eappen <neena.susaneappen at mail.utoronto.ca>
Sent: Tuesday, January 7, 2020 1:57 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: Re: [gmx-users] Simulated Annealing command line

Hi Kenny,

Thank you for your answer, but I did not understand clearly. For say 30 cycles of simulated annealing, what I have been doing currently is going through the following steps ( equilibration, annealing, production run, energy minimization) 30 times by changing names of input and output files every cycle.
My question is say after the 1st cycle, is there a way to input a single command line to repeat this process say the remaining 29 times by using energy minimized structure from the end of every cycle as the starting structure for the next cycle.

Any insight would be appreciated,

Thank you,

Neena Eappen
Graduate Student
Jockusch Lab<http://www.chem.utoronto.ca/wp/jockusch/>, U of T
________________________________
From: Neena Susan Eappen
Sent: Sunday, January 5, 2020 8:43 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] Simulated Annealing command line

Hello gromacs users,

For simulated annealing, I want to repeat cycle (equilibration, annealing, production run, energy minimization) say n times with the energy minimized structure from end of cycle 1 to be used as starting structure for cycle 2. I was wondering is there a way to do this as a loop with just one command line?

Many thanks,

Neena Eappen
Graduate Student
Jockusch Lab<http://www.chem.utoronto.ca/wp/jockusch/>, U of T

From alessandra.villa.biosim at gmail.com  Wed Jan  8 10:38:41 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Wed, 08 Jan 2020 09:38:41 -0000
Subject: [gmx-users] Make index command in gromacs
In-Reply-To: <CAChmq0iqZVt=d0eYaQ6xERamDAds4_ZXtdnW=ks2b_zqNKYt3g@mail.gmail.com>
References: <CAChmq0iqZVt=d0eYaQ6xERamDAds4_ZXtdnW=ks2b_zqNKYt3g@mail.gmail.com>
Message-ID: <CANogp5ygeaAS3Kf_Oiv7iF6mVTE+_zNkh7nx-kB1aT-R-Yea1w@mail.gmail.com>

Hi,

Maybe you could  use gmx select to generate your index file
http://manual.gromacs.org/documentation/current/onlinehelp/gmx-select.html?highlight=select

Best regards
Alessandra

On Tue, Jan 7, 2020 at 11:39 PM Shan Jayasinghe <
shanjayasinghe2011 at gmail.com> wrote:

> Dear Gromacs Users,
>
> In my simulations, I have different sizes of water droplets.  I need
> indexes of water molecules in each droplet separately. I am trying to make
> the  index file with gmx make_ndx, but I couldn't do it. Appreciate your
> help regarding this matter.
>
> Thank you.
> --
> Best Regards
> Shan Jayasinghe
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Wed Jan  8 10:38:41 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Wed, 08 Jan 2020 09:38:41 -0000
Subject: [gmx-users] Make index command in gromacs
In-Reply-To: <CAChmq0iqZVt=d0eYaQ6xERamDAds4_ZXtdnW=ks2b_zqNKYt3g@mail.gmail.com>
References: <CAChmq0iqZVt=d0eYaQ6xERamDAds4_ZXtdnW=ks2b_zqNKYt3g@mail.gmail.com>
Message-ID: <CANogp5ygeaAS3Kf_Oiv7iF6mVTE+_zNkh7nx-kB1aT-R-Yea1w@mail.gmail.com>

Hi,

Maybe you could  use gmx select to generate your index file
http://manual.gromacs.org/documentation/current/onlinehelp/gmx-select.html?highlight=select

Best regards
Alessandra

On Tue, Jan 7, 2020 at 11:39 PM Shan Jayasinghe <
shanjayasinghe2011 at gmail.com> wrote:

> Dear Gromacs Users,
>
> In my simulations, I have different sizes of water droplets.  I need
> indexes of water molecules in each droplet separately. I am trying to make
> the  index file with gmx make_ndx, but I couldn't do it. Appreciate your
> help regarding this matter.
>
> Thank you.
> --
> Best Regards
> Shan Jayasinghe
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From blau at kth.se  Wed Jan  8 10:39:15 2020
From: blau at kth.se (Christian Blau)
Date: Wed, 08 Jan 2020 09:39:15 -0000
Subject: [gmx-users] Make index command in gromacs
In-Reply-To: <CAChmq0iqZVt=d0eYaQ6xERamDAds4_ZXtdnW=ks2b_zqNKYt3g@mail.gmail.com>
References: <CAChmq0iqZVt=d0eYaQ6xERamDAds4_ZXtdnW=ks2b_zqNKYt3g@mail.gmail.com>
Message-ID: <46522240-0566-0c8e-b1d9-f7133b85bd52@kth.se>

Hi Shan,


gmx select gives you many more options to do complex arithmetic with selections that might help you here.


You can try using

gmx select -select "SELECTION STING"

you'll find lots of selection string examples at the bottom in here:

http://manual.gromacs.org/documentation/current/onlinehelp/selections.html



Best,

Christian


On 2020-01-07 23:33, Shan Jayasinghe wrote:
> Dear Gromacs Users,
>
> In my simulations, I have different sizes of water droplets.  I need
> indexes of water molecules in each droplet separately. I am trying to make
> the  index file with gmx make_ndx, but I couldn't do it. Appreciate your
> help regarding this matter.
>
> Thank you.

From navneetcdl at gmail.com  Wed Jan  8 10:39:49 2020
From: navneetcdl at gmail.com (Navneet Kumar)
Date: Wed, 08 Jan 2020 09:39:49 -0000
Subject: [gmx-users] Index group for Backbone/C-alpha of specific stretch of
	residues
Message-ID: <CAOvdM4W-5S2p8hKqGKy7-fsnbqz7Z0e4VBxHL+AwbA+zo7NPhg@mail.gmail.com>

Hello Everyone!


How to create an index group for Backbone/C-alpha for a specific set of
residues from protein? (Say Protein with 200 amino acid; want to create an
index group for the backbone of residues 150-210).
Regards
Navneet Kumar

From navneetcdl at gmail.com  Wed Jan  8 10:43:09 2020
From: navneetcdl at gmail.com (Navneet Kumar)
Date: Wed, 08 Jan 2020 09:43:09 -0000
Subject: [gmx-users] Index group for Backbone/C-alpha of specific
	stretch of residues
In-Reply-To: <CAOvdM4W-5S2p8hKqGKy7-fsnbqz7Z0e4VBxHL+AwbA+zo7NPhg@mail.gmail.com>
References: <CAOvdM4W-5S2p8hKqGKy7-fsnbqz7Z0e4VBxHL+AwbA+zo7NPhg@mail.gmail.com>
Message-ID: <CAOvdM4U-zTODkZSpHmvq2b87vgKx3f+yiGQbDcCKZrfYBuGW-A@mail.gmail.com>

Sorry, it should be 150-200 residues.

On Wed, Jan 8, 2020 at 3:09 PM Navneet Kumar <navneetcdl at gmail.com> wrote:

> Hello Everyone!
>
>
> How to create an index group for Backbone/C-alpha for a specific set of
> residues from protein? (Say Protein with 200 amino acid; want to create an
> index group for the backbone of residues 150-210).
> Regards
> Navneet Kumar
>
>
>
>
>
>

-- 






     Thanks & Regards
_______________________________________________________

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneetcdl at gmail.com  <navneetcdl at gmail.com>
<http://www.linkedin.com/in/navneet-kumar-74391814a/>
<http://facebook.com/xeon.singh> <http://instagram.com/snavneetkumar>

Please consider your environmental responsibility. Before printing this
e-mail message, ask yourself whether you really need a hard copy.

From blau at kth.se  Wed Jan  8 10:49:12 2020
From: blau at kth.se (Christian Blau)
Date: Wed, 08 Jan 2020 09:49:12 -0000
Subject: [gmx-users] Index group for Backbone/C-alpha of specific
 stretch of residues
In-Reply-To: <CAOvdM4U-zTODkZSpHmvq2b87vgKx3f+yiGQbDcCKZrfYBuGW-A@mail.gmail.com>
References: <CAOvdM4W-5S2p8hKqGKy7-fsnbqz7Z0e4VBxHL+AwbA+zo7NPhg@mail.gmail.com>
	<CAOvdM4U-zTODkZSpHmvq2b87vgKx3f+yiGQbDcCKZrfYBuGW-A@mail.gmail.com>
Message-ID: <922883ca-28a2-f6ca-9647-548baf78d43d@kth.se>

Hi Navnett,


gmx select will be your friend.


At the bottom of

http://manual.gromacs.org/documentation/current/onlinehelp/selections.html

you'll find some example commands. Something along the lines of

 ? gmx select -select 'name CA and resid > 149 and resid < 211'

should work.


It's a very powerful syntax and I figured for me it was very much worth the effort reading through that documentation.


Best,

Chrsitian

On 2020-01-08 10:42, Navneet Kumar wrote:
> Sorry, it should be 150-200 residues.
>
> On Wed, Jan 8, 2020 at 3:09 PM Navneet Kumar <navneetcdl at gmail.com> wrote:
>
>> Hello Everyone!
>>
>>
>> How to create an index group for Backbone/C-alpha for a specific set of
>> residues from protein? (Say Protein with 200 amino acid; want to create an
>> index group for the backbone of residues 150-210).
>> Regards
>> Navneet Kumar
>>
>>
>>
>>
>>
>>

From navneetcdl at gmail.com  Wed Jan  8 10:55:06 2020
From: navneetcdl at gmail.com (Navneet Kumar)
Date: Wed, 08 Jan 2020 09:55:06 -0000
Subject: [gmx-users] Index group for Backbone/C-alpha of specific
 stretch of residues
In-Reply-To: <922883ca-28a2-f6ca-9647-548baf78d43d@kth.se>
References: <CAOvdM4W-5S2p8hKqGKy7-fsnbqz7Z0e4VBxHL+AwbA+zo7NPhg@mail.gmail.com>
	<CAOvdM4U-zTODkZSpHmvq2b87vgKx3f+yiGQbDcCKZrfYBuGW-A@mail.gmail.com>
	<922883ca-28a2-f6ca-9647-548baf78d43d@kth.se>
Message-ID: <CAOvdM4VFXdAVWLPa+=JU5VD=s3DS=rBgH4GAwTgOGzgNoT6q-g@mail.gmail.com>

Thank You, Sir!

On Wed, Jan 8, 2020 at 3:19 PM Christian Blau <blau at kth.se> wrote:

> Hi Navnett,
>
>
> gmx select will be your friend.
>
>
> At the bottom of
>
> http://manual.gromacs.org/documentation/current/onlinehelp/selections.html
>
> you'll find some example commands. Something along the lines of
>
>    gmx select -select 'name CA and resid > 149 and resid < 211'
>
> should work.
>
>
> It's a very powerful syntax and I figured for me it was very much worth
> the effort reading through that documentation.
>
>
> Best,
>
> Chrsitian
>
> On 2020-01-08 10:42, Navneet Kumar wrote:
> > Sorry, it should be 150-200 residues.
> >
> > On Wed, Jan 8, 2020 at 3:09 PM Navneet Kumar <navneetcdl at gmail.com>
> wrote:
> >
> >> Hello Everyone!
> >>
> >>
> >> How to create an index group for Backbone/C-alpha for a specific set of
> >> residues from protein? (Say Protein with 200 amino acid; want to create
> an
> >> index group for the backbone of residues 150-210).
> >> Regards
> >> Navneet Kumar
> >>
> >>
> >>
> >>
> >>
> >>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.



-- 






     Thanks & Regards
_______________________________________________________

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneetcdl at gmail.com  <navneetcdl at gmail.com>
<http://www.linkedin.com/in/navneet-kumar-74391814a/>
<http://facebook.com/xeon.singh> <http://instagram.com/snavneetkumar>

Please consider your environmental responsibility. Before printing this
e-mail message, ask yourself whether you really need a hard copy.

From blau at kth.se  Wed Jan  8 10:55:08 2020
From: blau at kth.se (Christian Blau)
Date: Wed, 08 Jan 2020 09:55:08 -0000
Subject: [gmx-users] How to rotate the molecule in box
In-Reply-To: <e8683768-3c51-4cc5-b367-1b7dcf2378af.sunyeping@aliyun.com>
References: <e8683768-3c51-4cc5-b367-1b7dcf2378af.sunyeping@aliyun.com>
Message-ID: <a0124022-c509-6103-18b1-3cd14355d012@kth.se>

Hi Yeping,


The center of rotation is (0,0,0) for the rotate command, which is the lower left front corner of your box, and not the 
box center. That's why the molecule moves out of the box when rotating.

One (of conceivable more ways) to perform the rotation, is to use -center (0,0,0) to create a new structure, centered on 
the origin, then perform the rotation, and then shift the molecule back into the box center with -center only.


Best,

Christian


On 2019-12-30 14:44, sunyeping wrote:
> Dear all,
>
> By using the editconf command, we can build a box for the protein molecule, for example:
>
>       gmx editconf -f complex.gro -o newbox.gro -c -d 1.2 -bt cubic
>
> but how to rotate the molecule in the box? I tried to use "-rotate" option of the editconf command to do so, but I found part of the molecule goes out the pbc box after rotation. Please refer to the image at the following link:
>
> https://drive.google.com/file/d/1P_yTeRSkHpeUTXSUZMlTw2AHZ17s0htv/view?usp=sharing
>
> The molecule was orignally at position 1. I wanted to rotate the molecule around x and y axes by 45 degrees. After I ran the following command:
>
>      gmx editconf -f newbox.gro -rotate 45 45 0 -bt o -o newbpx_1.gro
>
> The molecule went to position 2. You can see part of the molecule are now out of the box.
>
> Do you know how to rotate the molecule but keep it within the box?
>
> Thank you in advance.
>
> Yeping

From devargyachakraborty.kgp at gmail.com  Wed Jan  8 11:12:08 2020
From: devargyachakraborty.kgp at gmail.com (Devargya Chakraborty)
Date: Wed, 08 Jan 2020 10:12:08 -0000
Subject: [gmx-users] cant compute msd
Message-ID: <CAJMw3wjBZOfxqY8+mFZ6qxCrGZ0WPOj35LpoQPCeZ==U-hA7CA@mail.gmail.com>

hi, when i am using the command
 gmx msd -f prd.xtc -n il.ndx -s out3.tpr -mol -o msd.xvg

after that choosing a group the following line is coming.
Select a group to calculate mean squared displacement for:
Group     0 (         System) has  5616 elements
Group     1 (          Other) has  5616 elements
Group     2 (             c2) has  2376 elements
Group     3 (           ntf2) has  3240 elements
Group     4 (              N) has   216 elements
Group     5 (              N) has   216 elements
Select a group: 3
Selected 3: 'ntf2'
Split group of 3240 atoms into 216 molecules
Reading frame    5000 time 20000.000   Killed

and i cant get the msd file any suggestion regarding this??

thank you

From blau at kth.se  Wed Jan  8 11:22:40 2020
From: blau at kth.se (Christian Blau)
Date: Wed, 08 Jan 2020 10:22:40 -0000
Subject: [gmx-users] cant compute msd
In-Reply-To: <CAJMw3wjBZOfxqY8+mFZ6qxCrGZ0WPOj35LpoQPCeZ==U-hA7CA@mail.gmail.com>
References: <CAJMw3wjBZOfxqY8+mFZ6qxCrGZ0WPOj35LpoQPCeZ==U-hA7CA@mail.gmail.com>
Message-ID: <eefe65cb-4e5f-210d-2b42-f900b7c18f2e@kth.se>

Hi Devargya,


I believe it's the mixture of -mol and -o options at the same time that leads to the unexpected behaviour - there can 
only be one .xvg output for this tool and we'll see to having it fixed.

Do you get any diff_mol.xvg files instead?


The documentation states that

"If -mol is set, gmx msd plots the MSD for individual molecules (including
making molecules whole across periodic boundaries): for each individual
molecule a diffusion constant is computed for its center of mass. The chosen
index group will be split into molecules."


Best,

Christian


On 2020-01-08 11:12, Devargya Chakraborty wrote:
> hi, when i am using the command
>   gmx msd -f prd.xtc -n il.ndx -s out3.tpr -mol -o msd.xvg
>
> after that choosing a group the following line is coming.
> Select a group to calculate mean squared displacement for:
> Group     0 (         System) has  5616 elements
> Group     1 (          Other) has  5616 elements
> Group     2 (             c2) has  2376 elements
> Group     3 (           ntf2) has  3240 elements
> Group     4 (              N) has   216 elements
> Group     5 (              N) has   216 elements
> Select a group: 3
> Selected 3: 'ntf2'
> Split group of 3240 atoms into 216 molecules
> Reading frame    5000 time 20000.000   Killed
>
> and i cant get the msd file any suggestion regarding this??
>
> thank you

From johannes.hermann at tum.de  Wed Jan  8 11:29:16 2020
From: johannes.hermann at tum.de (Johannes Hermann)
Date: Wed, 08 Jan 2020 10:29:16 -0000
Subject: [gmx-users] Position restrains calculation of virial
Message-ID: <fb36f9e7-e005-8769-cf37-d3783163287c@tum.de>

Dear all,

how is the virial computed when position restraints are applied? Are 
forces due to position restrains included or excluded?

Thanks!

All the best

Johannes

-- 
______________________________________
*Technische Universit?t M?nchen*
*Johannes Hermann, M.Sc.*
Lehrstuhl f?r Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

Email: johannes.hermann at tum.de

From yogesh.rma13 at gmail.com  Wed Jan  8 12:01:55 2020
From: yogesh.rma13 at gmail.com (Yogesh Sharma)
Date: Wed, 08 Jan 2020 11:01:55 -0000
Subject: [gmx-users] system has non zero net charge
Message-ID: <CACWq+6-OE3QXaYj0oxNSt_4t=V+gTT6vZe1xVHp6zVCQqV+OBQ@mail.gmail.com>

Greetings,
I am performing membrane protein simulation in the presence of a
biomolecule. topology for the molecule was downloaded from ATB server.
After simulation run, I found unexpected behviour of the added
biomolecule.  This ligand named UINL was showing affinity to ASP and GLU
residues. ligand didnt seperate through out simulation once bound, which is
highly unexpected at neutral pH.

I was getting these two notes during solvation.

Generated 1062 of the 3486 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein'
turning H bonds into constraints...
Excluding 3 bonded neighbours molecule type 'POPC'
turning H bonds into constraints...
Excluding 3 bonded neighbours molecule type 'U1NL'
turning H bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning H bonds into constraints...

NOTE 1 [file topol2.top, line 18875]:
  System has non-zero total charge: -1.000002
  Total charge should normally be an integer.

Is it possible this -1 charge is producing artifact. I have addded 20
molecules of same ligand in my system and 6 of them are binding to negative
charged residues.
I checked total charge on ligand.itp file, its zero. then i checked line
18875 in topol2.top its SOL which is highly unlikely to have any charge.

U1NL     3
[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  charge    mass
    1  HS14    1    U1NL     H4     1    0.480   1.0080
    2 OEOpt    1    U1NL     O4    2   -0.814  15.9994
    3    SI         1    U1NL     Si     3    1.336   28.0800
    4 OEOpt    1    U1NL     O1    4   -0.814  15.9994
    5  HS14     1    U1NL     H1     5    0.480   1.0080
    6 OEOpt    1    U1NL     O2    6   -0.814  15.9994
    7  HS14     1    U1NL     H3     7    0.480   1.0080
    8 OEOpt    1    U1NL     O3    8   -0.814  15.9994
    9  HS14    1    U1NL     H2     9    0.480   1.0080
; total charge of the molecule:  -0.000

How can i check what molecule is throwing this negative -1 charge to my
system?
Thankyou in advance for your valuable time.

From gudrun.gygli at kit.edu  Wed Jan  8 13:03:54 2020
From: gudrun.gygli at kit.edu (Gudrun Gygli)
Date: Wed, 08 Jan 2020 12:03:54 -0000
Subject: [gmx-users] system has non zero net charge
In-Reply-To: <CACWq+6-OE3QXaYj0oxNSt_4t=V+gTT6vZe1xVHp6zVCQqV+OBQ@mail.gmail.com>
References: <CACWq+6-OE3QXaYj0oxNSt_4t=V+gTT6vZe1xVHp6zVCQqV+OBQ@mail.gmail.com>
Message-ID: <265a83f3-a2d1-87f1-a62d-bc7f0b7cc9d5@kit.edu>

Hi Yogesh,

this happens to me as well sometimes, there are several options:

- your protein is not neutral (my best practice is to you use pdb2gmx 
interactively and set the charges for all amino acids manually following 
pkA predictions by e.g. Propka - then you will immediately know if the 
protien has a charge from the output)

- one of your itp files (I guess POPC and U1NL are from ATB) has a 
non-zero charge - make sure to show 10 decimal points when you calculate 
the total charge of all the atoms in the ligands, it happens sometimes 
that these do NOT add up to a completely neutral value, and rounding 
errors will occur and mess up the total charge of your system - 
especially if you add 20 identical molecules.... It is always a good 
idea to carefully check the parameters obtained from ATB or another 
server - mistakes happen!

- if the charge persists, you must neutralise the system using genion: 
http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-genion.html

Best of luck

Gudrun


Am 08.01.2020 um 12:01 schrieb Yogesh Sharma:
> Greetings,
> I am performing membrane protein simulation in the presence of a
> biomolecule. topology for the molecule was downloaded from ATB server.
> After simulation run, I found unexpected behviour of the added
> biomolecule.  This ligand named UINL was showing affinity to ASP and GLU
> residues. ligand didnt seperate through out simulation once bound, which is
> highly unexpected at neutral pH.
>
> I was getting these two notes during solvation.
>
> Generated 1062 of the 3486 non-bonded parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein'
> turning H bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'POPC'
> turning H bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'U1NL'
> turning H bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning H bonds into constraints...
>
> NOTE 1 [file topol2.top, line 18875]:
>    System has non-zero total charge: -1.000002
>    Total charge should normally be an integer.
>
> Is it possible this -1 charge is producing artifact. I have addded 20
> molecules of same ligand in my system and 6 of them are binding to negative
> charged residues.
> I checked total charge on ligand.itp file, its zero. then i checked line
> 18875 in topol2.top its SOL which is highly unlikely to have any charge.
>
> U1NL     3
> [ atoms ]
> ;  nr  type  resnr  resid  atom  cgnr  charge    mass
>      1  HS14    1    U1NL     H4     1    0.480   1.0080
>      2 OEOpt    1    U1NL     O4    2   -0.814  15.9994
>      3    SI         1    U1NL     Si     3    1.336   28.0800
>      4 OEOpt    1    U1NL     O1    4   -0.814  15.9994
>      5  HS14     1    U1NL     H1     5    0.480   1.0080
>      6 OEOpt    1    U1NL     O2    6   -0.814  15.9994
>      7  HS14     1    U1NL     H3     7    0.480   1.0080
>      8 OEOpt    1    U1NL     O3    8   -0.814  15.9994
>      9  HS14    1    U1NL     H2     9    0.480   1.0080
> ; total charge of the molecule:  -0.000
>
> How can i check what molecule is throwing this negative -1 charge to my
> system?
> Thankyou in advance for your valuable time.

From sadafrani6 at gmail.com  Wed Jan  8 13:29:27 2020
From: sadafrani6 at gmail.com (Sadaf Rani)
Date: Wed, 08 Jan 2020 12:29:27 -0000
Subject: [gmx-users] how to set system for absolute free enegy calculation
	of ligand in protein
Message-ID: <CAH9Uu9MAk+qPZCsNRL-ej8Bc9txhNij0p64VtXeZpaFgfuH2Ew@mail.gmail.com>

Dear Gromacs users
I need your suggestions regarding the calculation of free energy of binding
in of ligand protein-ligand complex in setting up the system.
I am performing binding free energy calculation following alchemical free
energy path. I added a single molecule type in topology for both protein
and ligand in order to add distance restraints between ligand and protein
atoms however for decoupling ligand from protein I need a separate molecule
type for the ligand.
How should I set the system to avoid this problem?

Thanks in advance.

Sadaf

From jalemkul at vt.edu  Wed Jan  8 13:49:10 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Wed, 08 Jan 2020 12:49:10 -0000
Subject: [gmx-users] Simulated Annealing command line
In-Reply-To: <YT1PR01MB3723D901A5AB97D9AE3A9856CD3F0@YT1PR01MB3723.CANPRD01.PROD.OUTLOOK.COM>
References: <YT1PR01MB37230F186B52FAD60AD177CFCD3D0@YT1PR01MB3723.CANPRD01.PROD.OUTLOOK.COM>
	<YT1PR01MB37230B3C02ADDF7983A0B987CD3F0@YT1PR01MB3723.CANPRD01.PROD.OUTLOOK.COM>
	<YT1PR01MB3723D901A5AB97D9AE3A9856CD3F0@YT1PR01MB3723.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <de050033-7fc2-7353-7a5e-5b9d03814be7@vt.edu>



On 1/7/20 6:35 PM, Neena Susan Eappen wrote:
> Hi Justin,
>
> Thank you for your answer. I haven't written scripts before, so I was wondering is there a sample script I can see for looping in gromacs.

What you're trying to do is similar to the logic in 
http://www.mdtutorials.com/gmx/membrane_protein/Files/run_inflategro.sh

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From jalemkul at vt.edu  Wed Jan  8 13:50:05 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Wed, 08 Jan 2020 12:50:05 -0000
Subject: [gmx-users] Index group for Backbone/C-alpha of specific
 stretch of residues
In-Reply-To: <922883ca-28a2-f6ca-9647-548baf78d43d@kth.se>
References: <CAOvdM4W-5S2p8hKqGKy7-fsnbqz7Z0e4VBxHL+AwbA+zo7NPhg@mail.gmail.com>
	<CAOvdM4U-zTODkZSpHmvq2b87vgKx3f+yiGQbDcCKZrfYBuGW-A@mail.gmail.com>
	<922883ca-28a2-f6ca-9647-548baf78d43d@kth.se>
Message-ID: <0e6f9056-c489-fd37-fdba-eea0a105783b@vt.edu>



On 1/8/20 4:49 AM, Christian Blau wrote:
> Hi Navnett,
>
>
> gmx select will be your friend.
>
>
> At the bottom of
>
> http://manual.gromacs.org/documentation/current/onlinehelp/selections.html 
>
>
> you'll find some example commands. Something along the lines of
>
> ? gmx select -select 'name CA and resid > 149 and resid < 211'
>
> should work.
>
>
> It's a very powerful syntax and I figured for me it was very much 
> worth the effort reading through that documentation.
>

It's also simple in make_ndx:

3 & r 150-210

Either way works. Whatever you find easier to use.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From jalemkul at vt.edu  Wed Jan  8 13:52:48 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Wed, 08 Jan 2020 12:52:48 -0000
Subject: [gmx-users] system has non zero net charge
In-Reply-To: <CACWq+6-OE3QXaYj0oxNSt_4t=V+gTT6vZe1xVHp6zVCQqV+OBQ@mail.gmail.com>
References: <CACWq+6-OE3QXaYj0oxNSt_4t=V+gTT6vZe1xVHp6zVCQqV+OBQ@mail.gmail.com>
Message-ID: <a68265b7-a114-f56d-1980-974ce4c38b84@vt.edu>



On 1/8/20 6:01 AM, Yogesh Sharma wrote:
> Greetings,
> I am performing membrane protein simulation in the presence of a
> biomolecule. topology for the molecule was downloaded from ATB server.
> After simulation run, I found unexpected behviour of the added
> biomolecule.  This ligand named UINL was showing affinity to ASP and GLU
> residues. ligand didnt seperate through out simulation once bound, which is
> highly unexpected at neutral pH.

Why is that unexpected? Your ligand is Si(OH)4 and likely participates 
in hydrogen-bonding interactions very easily with charged groups.

> I was getting these two notes during solvation.
>
> Generated 1062 of the 3486 non-bonded parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein'
> turning H bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'POPC'
> turning H bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'U1NL'
> turning H bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning H bonds into constraints...
>
> NOTE 1 [file topol2.top, line 18875]:
>    System has non-zero total charge: -1.000002
>    Total charge should normally be an integer.

The discrepancy between your value and -1 is simply due to rounding. The 
larger issue is you have a membrane system with a net charge. If you 
allow PME to apply a neutralizing background plasma to this system (i.e. 
you don't use counterions), you will get very severe artifacts.

> Is it possible this -1 charge is producing artifact. I have addded 20
> molecules of same ligand in my system and 6 of them are binding to negative
> charged residues.
> I checked total charge on ligand.itp file, its zero. then i checked line
> 18875 in topol2.top its SOL which is highly unlikely to have any charge.
> U1NL     3
> [ atoms ]
> ;  nr  type  resnr  resid  atom  cgnr  charge    mass
>      1  HS14    1    U1NL     H4     1    0.480   1.0080
>      2 OEOpt    1    U1NL     O4    2   -0.814  15.9994
>      3    SI         1    U1NL     Si     3    1.336   28.0800
>      4 OEOpt    1    U1NL     O1    4   -0.814  15.9994
>      5  HS14     1    U1NL     H1     5    0.480   1.0080
>      6 OEOpt    1    U1NL     O2    6   -0.814  15.9994
>      7  HS14     1    U1NL     H3     7    0.480   1.0080
>      8 OEOpt    1    U1NL     O3    8   -0.814  15.9994
>      9  HS14    1    U1NL     H2     9    0.480   1.0080
> ; total charge of the molecule:  -0.000
>
> How can i check what molecule is throwing this negative -1 charge to my
> system?

POPC is uncharged, water is uncharged, your ligand is uncharged, so the 
charge must be coming from...? :)

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From b.mijiddorj at gmail.com  Wed Jan  8 15:38:06 2020
From: b.mijiddorj at gmail.com (Mijiddorj B)
Date: Wed, 08 Jan 2020 14:38:06 -0000
Subject: [gmx-users] Vibrational spectra of amide I using gromacs
Message-ID: <CABgRApvj_E2KRG5N3xM72cFn4LvF6yudV+1uoNR=_cc0fq=j0w@mail.gmail.com>

Dear gmx users,

Hello, I would like to ask vibrational spectra of amide of specific
amino acids. Is it possible to analyze from classic MD calculations of
gromacs?
Or

Is there any software that is compatible with gmx trajectories  to
calculate the spectra?

Best regards,

Mijiddorj

From alessandra.villa.biosim at gmail.com  Wed Jan  8 15:52:44 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Wed, 08 Jan 2020 14:52:44 -0000
Subject: [gmx-users] Position restrains calculation of virial
In-Reply-To: <fb36f9e7-e005-8769-cf37-d3783163287c@tum.de>
References: <fb36f9e7-e005-8769-cf37-d3783163287c@tum.de>
Message-ID: <CANogp5z-vSpzuM62LbMZ2Qva=DsCvx-wnM8jhHF6tcsDkiSfcw@mail.gmail.com>

Hi Johannes,

On Wed, Jan 8, 2020 at 11:29 AM Johannes Hermann <johannes.hermann at tum.de>
wrote:

> Dear all,
>
> how is the virial computed when position restraints are applied? Are
> forces due to position restrains included or excluded?
>
>
Yes the the forces due to position restrains are included.

But I think that this does not necessary imply  that  the pressure is well
defined in NVT with position restrains
I recall that you had such a question a while ago
"Is the pressure well defined when I use position restrains
in NVT?"

Best regards
Alessandra

> Thanks!
>
> All the best
>
> Johannes
>
> --
> ______________________________________
> *Technische Universit?t M?nchen*
> *Johannes Hermann, M.Sc.*
> Lehrstuhl f?r Bioverfahrenstechnik
> Boltzmannstr. 15
> D-85748 Garching
> Tel: +49 8928915730
> Fax: +49 8928915714
>
> Email: johannes.hermann at tum.de
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

From alessandra.villa.biosim at gmail.com  Wed Jan  8 15:52:44 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Wed, 08 Jan 2020 14:52:44 -0000
Subject: [gmx-users] Position restrains calculation of virial
In-Reply-To: <fb36f9e7-e005-8769-cf37-d3783163287c@tum.de>
References: <fb36f9e7-e005-8769-cf37-d3783163287c@tum.de>
Message-ID: <CANogp5z-vSpzuM62LbMZ2Qva=DsCvx-wnM8jhHF6tcsDkiSfcw@mail.gmail.com>

Hi Johannes,

On Wed, Jan 8, 2020 at 11:29 AM Johannes Hermann <johannes.hermann at tum.de>
wrote:

> Dear all,
>
> how is the virial computed when position restraints are applied? Are
> forces due to position restrains included or excluded?
>
>
Yes the the forces due to position restrains are included.

But I think that this does not necessary imply  that  the pressure is well
defined in NVT with position restrains
I recall that you had such a question a while ago
"Is the pressure well defined when I use position restrains
in NVT?"

Best regards
Alessandra

> Thanks!
>
> All the best
>
> Johannes
>
> --
> ______________________________________
> *Technische Universit?t M?nchen*
> *Johannes Hermann, M.Sc.*
> Lehrstuhl f?r Bioverfahrenstechnik
> Boltzmannstr. 15
> D-85748 Garching
> Tel: +49 8928915730
> Fax: +49 8928915714
>
> Email: johannes.hermann at tum.de
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

From moura at ufscar.br  Wed Jan  8 16:00:59 2020
From: moura at ufscar.br (=?UTF-8?Q?Andr=C3=A9_Farias_de_Moura?=)
Date: Wed, 08 Jan 2020 15:00:59 -0000
Subject: [gmx-users] Vibrational spectra of amide I using gromacs
In-Reply-To: <CABgRApvj_E2KRG5N3xM72cFn4LvF6yudV+1uoNR=_cc0fq=j0w@mail.gmail.com>
References: <CABgRApvj_E2KRG5N3xM72cFn4LvF6yudV+1uoNR=_cc0fq=j0w@mail.gmail.com>
Message-ID: <CAKTwKgpjeN2PxhkYgmK8FS9UAHEeiSwnKuquYeF1jiyWyZwUfQ@mail.gmail.com>

Should be doable using any standard spreadsheet:

(1) save the bond lengths along the simulation for the bond of interest

(2) compute the time correlation function for these bond lengths (the
autocorrelation function for this time series)

(3) compute the Fourier transform of the time correlation function

Andre

On Wed, Jan 8, 2020 at 11:37 AM Mijiddorj B <b.mijiddorj at gmail.com> wrote:

> Dear gmx users,
>
> Hello, I would like to ask vibrational spectra of amide of specific
> amino acids. Is it possible to analyze from classic MD calculations of
> gromacs?
> Or
>
> Is there any software that is compatible with gmx trajectories  to
> calculate the spectra?
>
> Best regards,
>
> Mijiddorj
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>


-- 
_____________

Prof. Dr. Andr? Farias de Moura
Department of Chemistry
Federal University of S?o Carlos
S?o Carlos - Brazil
phone: +55-16-3351-8090

From moura at ufscar.br  Wed Jan  8 16:01:04 2020
From: moura at ufscar.br (=?UTF-8?Q?Andr=C3=A9_Farias_de_Moura?=)
Date: Wed, 08 Jan 2020 15:01:04 -0000
Subject: [gmx-users] Vibrational spectra of amide I using gromacs
In-Reply-To: <CABgRApvj_E2KRG5N3xM72cFn4LvF6yudV+1uoNR=_cc0fq=j0w@mail.gmail.com>
References: <CABgRApvj_E2KRG5N3xM72cFn4LvF6yudV+1uoNR=_cc0fq=j0w@mail.gmail.com>
Message-ID: <CAKTwKgpjeN2PxhkYgmK8FS9UAHEeiSwnKuquYeF1jiyWyZwUfQ@mail.gmail.com>

Should be doable using any standard spreadsheet:

(1) save the bond lengths along the simulation for the bond of interest

(2) compute the time correlation function for these bond lengths (the
autocorrelation function for this time series)

(3) compute the Fourier transform of the time correlation function

Andre

On Wed, Jan 8, 2020 at 11:37 AM Mijiddorj B <b.mijiddorj at gmail.com> wrote:

> Dear gmx users,
>
> Hello, I would like to ask vibrational spectra of amide of specific
> amino acids. Is it possible to analyze from classic MD calculations of
> gromacs?
> Or
>
> Is there any software that is compatible with gmx trajectories  to
> calculate the spectra?
>
> Best regards,
>
> Mijiddorj
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>


-- 
_____________

Prof. Dr. Andr? Farias de Moura
Department of Chemistry
Federal University of S?o Carlos
S?o Carlos - Brazil
phone: +55-16-3351-8090

From marcelodepolo at gmail.com  Wed Jan  8 16:26:07 2020
From: marcelodepolo at gmail.com (=?UTF-8?Q?Marcelo_Dep=C3=B3lo?=)
Date: Wed, 08 Jan 2020 15:26:07 -0000
Subject: [gmx-users] CMAP format on GROMACS
In-Reply-To: <mailman.459.1578364899.1966.gromacs.org_gmx-users@maillist.sys.kth.se>
References: <mailman.459.1578364899.1966.gromacs.org_gmx-users@maillist.sys.kth.se>
Message-ID: <CAFAAhpZKPJ=9RTxkx9mErkUUcata_8-3+bVrOr18d-nTQ30ixA@mail.gmail.com>

Thanks for your input, Justin. Helpful as always.


I am assuming the array is formatted to vary phi as a function of psi
i.e. (-180,-180), (-180,-165), (-180,-150) [considering (phi,psi)] and
again but for phi = -165.

I am also assuming that, since it is a 24x24 matrix, values will start in
phi=-180,psi=-180 but will end in phi=165, psi=165. Only a 25x25 matrix
would lead to end in phi=180,psi=180, but since they -180 and 180 are
equivalent, maybe GROMACS already do this workaround?

The last question: are those values in kJ/mol?

Cheers!
--
Marcelo


> The \ are line continuation characters, so GROMACS is reading a 24x24
> matrix in a single array of values.
>
> The values are written for all values of phi at a given value of psi,
> i.e. writing each row of the matrix, starting from phi = -180, psi =
> -180 until phi = 180, psi = 180.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 7 Jan 2020 11:40:30 +0900
> From: ??? <byunjy0614 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] The maxwarn fatal errors
> Message-ID: <4B64C77F-360F-44CA-B051-11DF14D7F2C7 at gmail.com>
> Content-Type: text/plain;       charset=us-ascii
>
> Dear everyone, Happy New year!
> I have gone through the Justin Lemku tutorial for Umbrella Sampling.
> During tutorial, When I treid to input the command line:
>   gmx grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -r
> npt0.gro -n index.ndx -o umbrella0.tpr
>
> I have met two warnings and they occured fatal error.:
>   Fatal error:
>   Too many warnings (2).
>    If you are sure all warnings are harmless, use the -maxwarn option.
>
> And the waring is:
>  WARNING 1 [file topol.top, line 56]:
>   The GROMOS force fields have been parametrized with a physically
>   incorrect multiple-time-stepping scheme for a twin-range cut-off. When
>   used with a single-range cut-off (or a correct Trotter
>   multiple-time-stepping scheme), physical properties, such as the density,
>   might differ from the intended values. Since there are researchers
>   actively working on validating GROMOS with modern integrators we have not
>   yet removed the GROMOS force fields, but you should be aware of these
>   issues and check if molecules in your system are affected before
>   proceeding. Further information is available at
>   https://redmine.gromacs.org/issues/2884 , and a longer explanation of
> our
>   decision to remove physically incorrect algorithms can be found at
>   https://doi.org/10.26434/chemrxiv.11474583.v1 .
>
>
> WARNING 2 [file md_umbrella.mdp]:
>   With Nose-Hoover T-coupling and Parrinello-Rahman p-coupling, tau-p (1)
>   should be at least twice as large as tau-t (1) to avoid resonances
>
> I solved this problem with using -maxwarn option but I am wondering
> whether thses warning is passed over.
> What do you think what I happend? dears. Any idea on what caused this
> problem?
>
> ------------------------------
>
> Message: 5
> Date: Mon, 6 Jan 2020 21:41:28 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] The maxwarn fatal errors
> Message-ID: <89785204-b49e-4f0c-3da9-10abd0b13d1c at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 1/6/20 9:40 PM, ??? wrote:
> > Dear everyone, Happy New year!
> > I have gone through the Justin Lemku tutorial for Umbrella Sampling.
> During tutorial, When I treid to input the command line:
> >    gmx grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -r
> npt0.gro -n index.ndx -o umbrella0.tpr
> >
> > I have met two warnings and they occured fatal error.:
> >    Fatal error:
> >    Too many warnings (2).
> >     If you are sure all warnings are harmless, use the -maxwarn option.
> >
> > And the waring is:
> >   WARNING 1 [file topol.top, line 56]:
> >    The GROMOS force fields have been parametrized with a physically
> >    incorrect multiple-time-stepping scheme for a twin-range cut-off. When
> >    used with a single-range cut-off (or a correct Trotter
> >    multiple-time-stepping scheme), physical properties, such as the
> density,
> >    might differ from the intended values. Since there are researchers
> >    actively working on validating GROMOS with modern integrators we have
> not
> >    yet removed the GROMOS force fields, but you should be aware of these
> >    issues and check if molecules in your system are affected before
> >    proceeding. Further information is available at
> >    https://redmine.gromacs.org/issues/2884 , and a longer explanation
> of our
> >    decision to remove physically incorrect algorithms can be found at
> >    https://doi.org/10.26434/chemrxiv.11474583.v1 .
> >
> >
> > WARNING 2 [file md_umbrella.mdp]:
> >    With Nose-Hoover T-coupling and Parrinello-Rahman p-coupling, tau-p
> (1)
> >    should be at least twice as large as tau-t (1) to avoid resonances
> >
> > I solved this problem with using -maxwarn option but I am wondering
> whether thses warning is passed over.
> > What do you think what I happend? dears. Any idea on what caused this
> problem?
>
> The first warning is very verbose and provides you with substantial
> justification and background reading.
>
> As for the second, change tau-p to 2 as suggested. Note that I have not
> made any attempt to update the tutorials for the 2020 version, and they
> are only guaranteed to be compatible with GROMACS 2018.x versions.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 189, Issue 13
> ******************************************************
>


-- 
--
Marcelo Dep?lo Pol?to
Postdoctoral Researcher
BIOAGRO - Room T07
Department of General Biology - UFV
Contact: + 55 31 3612-2464

From devargyachakraborty.kgp at gmail.com  Wed Jan  8 16:42:57 2020
From: devargyachakraborty.kgp at gmail.com (Devargya Chakraborty)
Date: Wed, 08 Jan 2020 15:42:57 -0000
Subject: [gmx-users] cant compute msd
In-Reply-To: <eefe65cb-4e5f-210d-2b42-f900b7c18f2e@kth.se>
References: <CAJMw3wjBZOfxqY8+mFZ6qxCrGZ0WPOj35LpoQPCeZ==U-hA7CA@mail.gmail.com>
	<eefe65cb-4e5f-210d-2b42-f900b7c18f2e@kth.se>
Message-ID: <CAJMw3wiamLbs9kLBCa+0Th_7Q3vZNo7yj4LS6JXR1Jgz_zDcNg@mail.gmail.com>

After removing the -mol command it worked fine.

On Wed, Jan 8, 2020, 3:53 PM Christian Blau <blau at kth.se> wrote:

> Hi Devargya,
>
>
> I believe it's the mixture of -mol and -o options at the same time that
> leads to the unexpected behaviour - there can
> only be one .xvg output for this tool and we'll see to having it fixed.
>
> Do you get any diff_mol.xvg files instead?
>
>
> The documentation states that
>
> "If -mol is set, gmx msd plots the MSD for individual molecules (including
> making molecules whole across periodic boundaries): for each individual
> molecule a diffusion constant is computed for its center of mass. The
> chosen
> index group will be split into molecules."
>
>
> Best,
>
> Christian
>
>
> On 2020-01-08 11:12, Devargya Chakraborty wrote:
> > hi, when i am using the command
> >   gmx msd -f prd.xtc -n il.ndx -s out3.tpr -mol -o msd.xvg
> >
> > after that choosing a group the following line is coming.
> > Select a group to calculate mean squared displacement for:
> > Group     0 (         System) has  5616 elements
> > Group     1 (          Other) has  5616 elements
> > Group     2 (             c2) has  2376 elements
> > Group     3 (           ntf2) has  3240 elements
> > Group     4 (              N) has   216 elements
> > Group     5 (              N) has   216 elements
> > Select a group: 3
> > Selected 3: 'ntf2'
> > Split group of 3240 atoms into 216 molecules
> > Reading frame    5000 time 20000.000   Killed
> >
> > and i cant get the msd file any suggestion regarding this??
> >
> > thank you
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From catjmc at gmail.com  Wed Jan  8 17:00:13 2020
From: catjmc at gmail.com (Jimmy Chen)
Date: Wed, 08 Jan 2020 16:00:13 -0000
Subject: [gmx-users] is GPU peer access(RDMA) supported with inter-node and
 gmx2020 mpi version?
Message-ID: <CAEZo3OMSbPABK_tdLaYF2O2oTnJgY6GBq_cTO_4WXoLL04r+fg@mail.gmail.com>

Hi,

is GPU peer access(RDMA) supported with inter-node and gmx2020 mpi version
on NVidia GPU?
or just work only in single-node with threadMPI via Nvidia GPU direct?

Thanks,
Jimmy

From matthew.fisher at stcatz.ox.ac.uk  Wed Jan  8 17:12:50 2020
From: matthew.fisher at stcatz.ox.ac.uk (Matthew Fisher)
Date: Wed, 08 Jan 2020 16:12:50 -0000
Subject: [gmx-users] Comparing the RMSD of an in silico variant to a crystal
	structure.
Message-ID: <LNXP265MB1516C116B7449C01F3CA46A38F3E0@LNXP265MB1516.GBRP265.PROD.OUTLOOK.COM>

Dear all,

I'm simulating the effect of amino acid mutations on tertiary structure and, for benchmarking purposes, I want to compare the RMS of my in silico variant trajectories (prepared from the WT structure) to their cystallographic structures.

In the gmx rms command, when I select the structure for the -s flag, should I use the pdb file from the RCSB, or alternatively should I take the crystal structure, parametise it using pdb2gmx and then take the pre-minimisation .tpr file? Alternatively is there something else I should be doing? Any advice would be appreciated.

Best wishes,
Matthew



From 177cy500.bratin at nitk.edu.in  Wed Jan  8 17:31:41 2020
From: 177cy500.bratin at nitk.edu.in (Bratin Kumar Das)
Date: Wed, 08 Jan 2020 16:31:41 -0000
Subject: [gmx-users] Comparing the RMSD of an in silico variant to a
 crystal structure.
In-Reply-To: <LNXP265MB1516C116B7449C01F3CA46A38F3E0@LNXP265MB1516.GBRP265.PROD.OUTLOOK.COM>
References: <LNXP265MB1516C116B7449C01F3CA46A38F3E0@LNXP265MB1516.GBRP265.PROD.OUTLOOK.COM>
Message-ID: <CAM7TW5viDnRc3xM8zrUUfcapWw7T2X268-r0U2byhTJPeHN+Zw@mail.gmail.com>

Use the .tpr file generated by grompp module

On Wed 8 Jan, 2020, 9:43 PM Matthew Fisher, <matthew.fisher at stcatz.ox.ac.uk>
wrote:

> Dear all,
>
> I'm simulating the effect of amino acid mutations on tertiary structure
> and, for benchmarking purposes, I want to compare the RMS of my in silico
> variant trajectories (prepared from the WT structure) to their
> cystallographic structures.
>
> In the gmx rms command, when I select the structure for the -s flag,
> should I use the pdb file from the RCSB, or alternatively should I take the
> crystal structure, parametise it using pdb2gmx and then take the
> pre-minimisation .tpr file? Alternatively is there something else I should
> be doing? Any advice would be appreciated.
>
> Best wishes,
> Matthew
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From b.mijiddorj at gmail.com  Thu Jan  9 01:15:11 2020
From: b.mijiddorj at gmail.com (Mijiddorj B)
Date: Thu, 09 Jan 2020 00:15:11 -0000
Subject: [gmx-users] gromacs.org_gmx-users Digest, Vol 189, Issue 18
In-Reply-To: <mailman.488.1578498177.1966.gromacs.org_gmx-users@maillist.sys.kth.se>
References: <mailman.488.1578498177.1966.gromacs.org_gmx-users@maillist.sys.kth.se>
Message-ID: <CABgRApuG7jPVzXhUpLysWrVYtZfv+4fN-FH6OzFEg6Oj8rFLdQ@mail.gmail.com>

Dear Andre

Thank you very much for your quick response.
I am very new for this type of analysis, and I would like to ask further. I
am sorry for that. Is there any good software?
If you have any experience, please suggest me some useful software for the
time series correlation and the Fourier transformation.

Best regards,

Mijiddorj

>
> Should be doable using any standard spreadsheet:
>
> (1) save the bond lengths along the simulation for the bond of interest
>
> (2) compute the time correlation function for these bond lengths (the
> autocorrelation function for this time series)
>
> (3) compute the Fourier transform of the time correlation function
>
> Andre
>
> On Wed, Jan 8, 2020 at 11:37 AM Mijiddorj B <b.mijiddorj at gmail.com> wrote:
>
> > Dear gmx users,
> >
> > Hello, I would like to ask vibrational spectra of amide of specific
> > amino acids. Is it possible to analyze from classic MD calculations of
> > gromacs?
> > Or
> >
> > Is there any software that is compatible with gmx trajectories  to
> > calculate the spectra?
> >
> > Best regards,
> >
> > Mijiddorj
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> --
> _____________
>
> Prof. Dr. Andr? Farias de Moura
> Department of Chemistry
> Federal University of S?o Carlos
> S?o Carlos - Brazil
> phone: +55-16-3351-8090
>
>
> ------------------------------
>

From b.mijiddorj at gmail.com  Thu Jan  9 01:18:32 2020
From: b.mijiddorj at gmail.com (Mijiddorj B)
Date: Thu, 09 Jan 2020 00:18:32 -0000
Subject: [gmx-users] Vibrational spectra of amide I using gromacs
In-Reply-To: <mailman.488.1578498177.1966.gromacs.org_gmx-users@maillist.sys.kth.se>
References: <mailman.488.1578498177.1966.gromacs.org_gmx-users@maillist.sys.kth.se>
Message-ID: <CABgRAptUqzb2Kv7CGX4xOvgfLDwU2M_aC_2iAYtPAOrPaY-u3Q@mail.gmail.com>

Dear Andre

Thank you very much for your quick response.
I am very new for this type of analysis, and I would like to ask further. I
am sorry for that. Is there any good software?
If you have any experience, please suggest me some useful software for the
time series correlation and the Fourier transformation.

Best regards,

Mijiddorj

Should be doable using any standard spreadsheet:
>
> (1) save the bond lengths along the simulation for the bond of interest
>
> (2) compute the time correlation function for these bond lengths (the
> autocorrelation function for this time series)
>
> (3) compute the Fourier transform of the time correlation function
>
> Andre
>
> On Wed, Jan 8, 2020 at 11:37 AM Mijiddorj B <b.mijiddorj at gmail.com> wrote:
>
> > Dear gmx users,
> >
> > Hello, I would like to ask vibrational spectra of amide of specific
> > amino acids. Is it possible to analyze from classic MD calculations of
> > gromacs?
> > Or
> >
> > Is there any software that is compatible with gmx trajectories  to
> > calculate the spectra?
> >
> > Best regards,
> >
> > Mijiddorj
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> --
> _____________
>
> Prof. Dr. Andr? Farias de Moura
> Department of Chemistry
> Federal University of S?o Carlos
> S?o Carlos - Brazil
> phone: +55-16-3351-8090
>
>
> ------------------------------
>
>
>

From moura at ufscar.br  Thu Jan  9 02:34:11 2020
From: moura at ufscar.br (=?UTF-8?Q?Andr=C3=A9_Farias_de_Moura?=)
Date: Thu, 09 Jan 2020 01:34:11 -0000
Subject: [gmx-users] Vibrational spectra of amide I using gromacs
In-Reply-To: <CABgRAptUqzb2Kv7CGX4xOvgfLDwU2M_aC_2iAYtPAOrPaY-u3Q@mail.gmail.com>
References: <mailman.488.1578498177.1966.gromacs.org_gmx-users@maillist.sys.kth.se>
	<CABgRAptUqzb2Kv7CGX4xOvgfLDwU2M_aC_2iAYtPAOrPaY-u3Q@mail.gmail.com>
Message-ID: <CAKTwKgrecyH10WMA+Sw_86rHyoP9c6k2XsPknvYoEwiUfkyL1g@mail.gmail.com>

Dear Mijiddorj,

It is a matter of taste, but I like to use xmgrace for that kind of
analysis.

The GROMACS tool gmx analyze can do that for you:
http://manual.gromacs.org/documentation/5.1/onlinehelp/gmx-analyze.html

Andre

On Wed, Jan 8, 2020 at 9:18 PM Mijiddorj B <b.mijiddorj at gmail.com> wrote:

> Dear Andre
>
> Thank you very much for your quick response.
> I am very new for this type of analysis, and I would like to ask further. I
> am sorry for that. Is there any good software?
> If you have any experience, please suggest me some useful software for the
> time series correlation and the Fourier transformation.
>
> Best regards,
>
> Mijiddorj
>
> Should be doable using any standard spreadsheet:
> >
> > (1) save the bond lengths along the simulation for the bond of interest
> >
> > (2) compute the time correlation function for these bond lengths (the
> > autocorrelation function for this time series)
> >
> > (3) compute the Fourier transform of the time correlation function
> >
> > Andre
> >
> > On Wed, Jan 8, 2020 at 11:37 AM Mijiddorj B <b.mijiddorj at gmail.com>
> wrote:
> >
> > > Dear gmx users,
> > >
> > > Hello, I would like to ask vibrational spectra of amide of specific
> > > amino acids. Is it possible to analyze from classic MD calculations of
> > > gromacs?
> > > Or
> > >
> > > Is there any software that is compatible with gmx trajectories  to
> > > calculate the spectra?
> > >
> > > Best regards,
> > >
> > > Mijiddorj
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> >
> >
> > --
> > _____________
> >
> > Prof. Dr. Andr? Farias de Moura
> > Department of Chemistry
> > Federal University of S?o Carlos
> > S?o Carlos - Brazil
> > phone: +55-16-3351-8090
> >
> >
> > ------------------------------
> >
> >
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>


-- 
_____________

Prof. Dr. Andr? Farias de Moura
Department of Chemistry
Federal University of S?o Carlos
S?o Carlos - Brazil
phone: +55-16-3351-8090

From jalemkul at vt.edu  Thu Jan  9 03:43:59 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Thu, 09 Jan 2020 02:43:59 -0000
Subject: [gmx-users] Comparing the RMSD of an in silico variant to a
 crystal structure.
In-Reply-To: <LNXP265MB1516C116B7449C01F3CA46A38F3E0@LNXP265MB1516.GBRP265.PROD.OUTLOOK.COM>
References: <LNXP265MB1516C116B7449C01F3CA46A38F3E0@LNXP265MB1516.GBRP265.PROD.OUTLOOK.COM>
Message-ID: <5dbde9e1-0225-7a2a-2a1d-e63dda5f7717@vt.edu>



On 1/8/20 11:12 AM, Matthew Fisher wrote:
> Dear all,
>
> I'm simulating the effect of amino acid mutations on tertiary structure and, for benchmarking purposes, I want to compare the RMS of my in silico variant trajectories (prepared from the WT structure) to their cystallographic structures.
>
> In the gmx rms command, when I select the structure for the -s flag, should I use the pdb file from the RCSB, or alternatively should I take the crystal structure, parametise it using pdb2gmx and then take the pre-minimisation .tpr file? Alternatively is there something else I should be doing? Any advice would be appreciated.

The latter is the best approach as it will allow for proper 
mass-weighting in the RMSD calculation.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From jalemkul at vt.edu  Thu Jan  9 03:44:47 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Thu, 09 Jan 2020 02:44:47 -0000
Subject: [gmx-users] CMAP format on GROMACS
In-Reply-To: <CAFAAhpZKPJ=9RTxkx9mErkUUcata_8-3+bVrOr18d-nTQ30ixA@mail.gmail.com>
References: <mailman.459.1578364899.1966.gromacs.org_gmx-users@maillist.sys.kth.se>
	<CAFAAhpZKPJ=9RTxkx9mErkUUcata_8-3+bVrOr18d-nTQ30ixA@mail.gmail.com>
Message-ID: <8708897b-9d3e-f8fd-7812-3e684448ab61@vt.edu>



On 1/8/20 10:25 AM, Marcelo Dep?lo wrote:
> Thanks for your input, Justin. Helpful as always.
>
>
> I am assuming the array is formatted to vary phi as a function of psi
> i.e. (-180,-180), (-180,-165), (-180,-150) [considering (phi,psi)] and
> again but for phi = -165.
>
> I am also assuming that, since it is a 24x24 matrix, values will start in
> phi=-180,psi=-180 but will end in phi=165, psi=165. Only a 25x25 matrix
> would lead to end in phi=180,psi=180, but since they -180 and 180 are
> equivalent, maybe GROMACS already do this workaround?

+/- 180 are understood to be equivalent.

> The last question: are those values in kJ/mol?

Yes. GROMACS always uses SI units.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From prasanthghanta at sssihl.edu.in  Thu Jan  9 11:55:19 2020
From: prasanthghanta at sssihl.edu.in (Prasanth G, Research Scholar)
Date: Thu, 09 Jan 2020 10:55:19 -0000
Subject: [gmx-users] charting Ligand's movement in the binding pocket
Message-ID: <CAGpSbST6upTfhf6nhfFF5bRR8uvu+U3BEqFJMsRwDHM8Xy1Wiw@mail.gmail.com>

Dear All,

I am interested in charting the trajectory of the ligand with respect to
the residues of the binding pocket, during the simulation.
May be representing the center of mass of the ligand as a dot at each
frame, would help us see the path traced by the ligand in the pocket,
during the simulation. Is there a possibility to do this during the
trajectory analysis period / post production..?
I was wondering if we could perform PCA and impose the ligand's trajectory
on the bound complex and visualize only the ligand's movement with respect
to the amino acid residues of the binding pocket. But this would not give a
clear idea as the residues in binding pocket also move during the course of
simulation.
Hoping that i was able to explain it well enough..
Thank you in advance.

-- 
Regards,
Prasanth.

From aa.hind at hotmail.com  Thu Jan  9 14:58:57 2020
From: aa.hind at hotmail.com (hind ahmed)
Date: Thu, 09 Jan 2020 13:58:57 -0000
Subject: [gmx-users] Replica exchange probabilities and extend simulation
Message-ID: <DB8PR10MB26498147F3CBFE59B8ACF839EA390@DB8PR10MB2649.EURPRD10.PROD.OUTLOOK.COM>

Dear All,

 Are these probabilities good? and how can I extend the simulation of replica-exchange?

Thanks

Replica exchange statistics
Repl  14999 attempts, 7500 odd, 7499 even
Repl  average probabilities:
Repl     0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31
Repl      .03  .04  .04  .04  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .02  .02  .02  .01  .02  .02  .02  .02  .02
Repl  number of exchanges:
Repl     0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31
Repl      259  263  270  330   62   57   63   58   65   67   71   74   89   87   88  103  100  103   98   98  114   93  132  127  149  111  117  126  129  124  145
Repl  average number of exchanges:
Repl     0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31
Repl      .03  .04  .04  .04  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .02  .01  .02  .02  .02  .01  .02  .02  .02  .02  .02


From aa.hind at hotmail.com  Thu Jan  9 15:01:57 2020
From: aa.hind at hotmail.com (hind ahmed)
Date: Thu, 09 Jan 2020 14:01:57 -0000
Subject: [gmx-users] Visualize replica exchange
Message-ID: <DB8PR10MB26495E9BC7CDB127F3170533EA390@DB8PR10MB2649.EURPRD10.PROD.OUTLOOK.COM>

Dear All,

How can I visualize replica exchange in VMD?

Thanks

From navneetcdl at gmail.com  Thu Jan  9 15:42:45 2020
From: navneetcdl at gmail.com (Navneet Kumar)
Date: Thu, 09 Jan 2020 14:42:45 -0000
Subject: [gmx-users] Index group for Backbone/C-alpha of specific
 stretch of residues
In-Reply-To: <0e6f9056-c489-fd37-fdba-eea0a105783b@vt.edu>
References: <CAOvdM4W-5S2p8hKqGKy7-fsnbqz7Z0e4VBxHL+AwbA+zo7NPhg@mail.gmail.com>
	<CAOvdM4U-zTODkZSpHmvq2b87vgKx3f+yiGQbDcCKZrfYBuGW-A@mail.gmail.com>
	<922883ca-28a2-f6ca-9647-548baf78d43d@kth.se>
	<0e6f9056-c489-fd37-fdba-eea0a105783b@vt.edu>
Message-ID: <CAOvdM4XkZY_ANmne9WRi1-Mva8GmdD_AycL0Uw=Lge8MU2qQMQ@mail.gmail.com>

Thank You, sir!

What If I want to extend the residues like choose c-alpha of 150-200 &
60-70 in a single index group ?


On Wed, Jan 8, 2020 at 6:21 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/8/20 4:49 AM, Christian Blau wrote:
> > Hi Navnett,
> >
> >
> > gmx select will be your friend.
> >
> >
> > At the bottom of
> >
> >
> http://manual.gromacs.org/documentation/current/onlinehelp/selections.html
> >
> >
> > you'll find some example commands. Something along the lines of
> >
> >   gmx select -select 'name CA and resid > 149 and resid < 211'
> >
> > should work.
> >
> >
> > It's a very powerful syntax and I figured for me it was very much
> > worth the effort reading through that documentation.
> >
>
> It's also simple in make_ndx:
>
> 3 & r 150-210
>
> Either way works. Whatever you find easier to use.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.



-- 






     Thanks & Regards
_______________________________________________________

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneetcdl at gmail.com  <navneetcdl at gmail.com>
<http://www.linkedin.com/in/navneet-kumar-74391814a/>
<http://facebook.com/xeon.singh> <http://instagram.com/snavneetkumar>

Please consider your environmental responsibility. Before printing this
e-mail message, ask yourself whether you really need a hard copy.

From pall.szilard at gmail.com  Thu Jan  9 17:03:56 2020
From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=)
Date: Thu, 09 Jan 2020 16:03:56 -0000
Subject: [gmx-users] is GPU peer access(RDMA) supported with inter-node
 and gmx2020 mpi version?
In-Reply-To: <CAEZo3OMSbPABK_tdLaYF2O2oTnJgY6GBq_cTO_4WXoLL04r+fg@mail.gmail.com>
References: <CAEZo3OMSbPABK_tdLaYF2O2oTnJgY6GBq_cTO_4WXoLL04r+fg@mail.gmail.com>
Message-ID: <CANnYEw7r7QcNi44j4O1XcZGo+RqwX-YudBtQomma-CTZPqjowA@mail.gmail.com>

On Wed, Jan 8, 2020 at 5:00 PM Jimmy Chen <catjmc at gmail.com> wrote:

> Hi,
>
> is GPU peer access(RDMA) supported with inter-node and gmx2020 mpi version
> on NVidia GPU?
>

No, that is currently not implemented.

Cheers,
--
Szil?rd

or just work only in single-node with threadMPI via Nvidia GPU direct?
>
> Thanks,
> Jimmy
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From pall.szilard at gmail.com  Thu Jan  9 17:10:59 2020
From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=)
Date: Thu, 09 Jan 2020 16:10:59 -0000
Subject: [gmx-users] Gromacs 2019 - Ryzen Architecture
In-Reply-To: <CAEJMVeum9CB9ygf9r36F9+C8bXCwL2GuCpgVJBo648YO1eS8dw@mail.gmail.com>
References: <2f123e28-d6bb-4958-8eab-85f8a1158a14@fu-berlin.de>
	<44a30732-2788-f60e-ecca-58959a63dc19@gmail.com>
	<CAEJMVeum9CB9ygf9r36F9+C8bXCwL2GuCpgVJBo648YO1eS8dw@mail.gmail.com>
Message-ID: <CANnYEw6mOXmMd-NXDoq6O99sLiDJtAm31uT2ZJmEdJchiEff5A@mail.gmail.com>

Good catch Kevin, that is likely an issue -- at least part of it.

Note that you can also use the mdrun -multidir functionality to avoid
having to manually manage mdrun process placement and pinning.

Another aspect is that if you leave half of the CPU cores unused, the cores
in use can boost to a higher clock rate and therefore can complete the work
on the CPU quicker which, as part of this work does not overlap with the
GPU, will impact the fraction of the time the GPU will be idle (and hence
also the time the GPU will be busy). For a fair comparison, run something
on those otherwise idle cores (at least a "stress -c 8" or possibly a
CPU-only mdrun); generally this is how we evaluate performance as a
function of CPU cores per GPU).

Cheers,
--
Szil?rd


On Sat, Jan 4, 2020 at 9:11 PM Kevin Boyd <kevin.boyd at uconn.edu> wrote:

> Hi,
>
> A few things besides any Ryzen-specific issues. First, your pinoffset for
> the second one should be 16, not 17. The way yours is set up, you're
> running on cores 0-15, then Gromacs will detect that your second
> simulation parameters are invalid (because from cores 17-32, core 32 does
> not exist) and turn off core pinning. You can verify that in the log file.
>
> Second, 16 threads per simulation is overkill, and you can get gains from
> stealing from GPU down-time by running 2 simulations per GPU. So I would
> suggest something like
>
> mdrun -nt 8 -pin on -pinoffset 0 -gpu_id 0 &
> mdrun -nt 8 -pin on -pinoffset 8 -gpu_id 0 &
> mdrun -nt 8 -pin on -pinoffset 16 -gpu_id 1 &
> mdrun -nt 8 -pin on -pinoffset 24 -gpu_id 1
>
> might give you close to optimal performance.
>
> On Thu, Jan 2, 2020 at 5:32 AM Paul bauer <paul.bauer.q at gmail.com> wrote:
>
> > Hello,
> >
> > we only added full detection and support for the newer Rizen chip-sets
> > with GROMACS 2019.5, so please try if the update to this version solves
> > your issue.
> > If not, please open an issue on redmine.gromacs.org so we can track the
> > problem and try to solve it.
> >
> > Cheers
> >
> > Paul
> >
> > On 02/01/2020 13:26, Sandro Wrzalek wrote:
> > > Hi,
> > >
> > > happy new year!
> > >
> > > Now to my problem:
> > >
> > > I use Gromacs 2019.3 and to try to run some simulations (roughly 30k
> > > atoms per system) on my PC which has the following configuration:
> > >
> > > CPU: Ryzen 3950X (overclocked to 4.1 GHz)
> > >
> > > GPU #1: Nvidia RTX 2080 Ti
> > >
> > > GPU #2: Nvidia RTX 2080 Ti
> > >
> > > RAM: 64 GB
> > >
> > > PSU: 1600 Watts
> > >
> > >
> > > Each run uses one GPU and 16 of 32 logical cores. Doing only one run
> > > at time (gmx mdrun -deffnm rna0 -gpu_id 0 -nb gpu -pme gpu) the GPU
> > > utilization is roughly around 84% but if I add a second run, the
> > > utilization of both GPUs drops to roughly 20%, while leaving logical
> > > cores 17-32 idle (I changed parameter gpu_id, accordingly).
> > >
> > > Adding additional parameters for each run:
> > >
> > > gmx mdrun -deffnm rna0 -nt 16 -pin on -pinoffset 0 -gpu_id 0 -nb gpu
> > > -pme gpu
> > >
> > > gmx mdrun -deffnm rna0 -nt 16 -pin on -pinoffset 17 -gpu_id 1 -nb gpu
> > > -pme gpu
> > >
> > > I get a utilization of 78% per GPU, which is nice but not near the 84%
> > > I got with only one run. In theory, however, it should come at least
> > > close to that utilization.
> > >
> > > I suspect, the Ryzen Chiplet design as the culprit since Gromacs seems
> > > to prefer the the first Chiplet, even if two simultaneous simulations
> > > have the resources to occupy both. The reason for the 78% utilization
> > > could be because of overhead between the two Chiplets via the infinity
> > > band. However, I have no proof, nor am I able to explain why gmx mdrun
> > > -deffnm rna0 -nt 16 -gpu_id 0 & 1 -nb gpu -pme gpu works as well -
> > > seems to occupy free logical cores then.
> > >
> > > Long story short:
> > >
> > > Are there any workarounds to squeeze the last bit out of my setup? Is
> > > it possible to choose the logical cores manually (I did not found
> > > anything in the docs so far)?
> > >
> > >
> > > Thank you for your help!
> > >
> > >
> > > Best,
> > >
> > > Sandro
> > >
> >
> > --
> > Paul Bauer, PhD
> > GROMACS Development Manager
> > KTH Stockholm, SciLifeLab
> > 0046737308594
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From bjoern at cellmicrocosmos.org  Thu Jan  9 22:41:07 2020
From: bjoern at cellmicrocosmos.org (=?UTF-8?Q?Bj=c3=b6rn_Sommer?=)
Date: Thu, 09 Jan 2020 21:41:07 -0000
Subject: [gmx-users] CfP EuroVis 2020 Workshop on Molecular Graphics and
 Visual Analysis of Molecular Data
Message-ID: <ab35f540-5c8e-28bc-7c6f-4c2aaa1cffea@cellmicrocosmos.org>

*Workshop on Molecular Graphics and Visual Analysis of Molecular Data *

*

(co-located with EuroVis & Eurographics 2020)

May 25th, 2020, Norrk?ping, Sweden

************************************************************************************

?

Molecular visualization and graphics is one of the oldest branches of
scientific visualization, which has been developing for over 50 years.
Due to the continuous advances in both computational biology and
computer graphics techniques, molecular graphics and visualization are
very active areas of research. Not only the ever-increasing dataset
sizes yield a constant challenge for visual analysis, but also new
technologies like advances in web-based graphics or augmented and
virtual reality open new possibilities. This half-day multidisciplinary
workshop - which is held in conjunction with EuroVis for the third time
and with Eurographics for the first time - brings together visualization
and computer graphics researchers working with molecular data.


Whereas molecular graphics is an established topic for many years, the
hybrid-dimensional visual analysis of molecular structures is still a
quite new research field with a lot of potential. We would like to
encourage submissions especially using new technologies, such as
immersive analytics or ML-related approaches.


We invite short papers as well as full papers (2-4 pages for short and
up to 8 pages for full papers, both with an additional page reserved for
references). All papers will undergo a single-stage, double-blind peer
review process. Accepted papers will be published in the EG digital
library. The workshop will be held in Norrk?ping, Sweden, May 25th,
2020, as part of EuroVis & Eurographics 2020.

??

Suggested topics include, but are not limited to:

- Molecular Graphics & Rendering

- Web-based Molecular Graphics & Visualization

- Immersive Analytics approaches using, e.g., VR/AR technologies

- Visual Analysis of Molecular Data (e.g., molecular structures,
biological networks, and pathways, or omics data)

- Visualization of Dynamic Molecular Data & Large Molecular Systems

- Tools papers describing new molecular visualization tools or novel
features in existing tools?

?

More info:

https://tinyurl.com/molva

?

Important Dates

************************************************************************

Paper Submission Deadline:February 21, 2020

Notification of Acceptance:March 24, 2020

Camera-ready Deadline:April 8, 2020

Workshop Date:May 25, 2020

?

Organizers and Contact

************************************************************************

- Jan Byska, University of Bergen, Norway

- Michael Krone, University of T?bingen, Germany

- Bjorn Sommer, Royal College of Art, UK

?

If you have any questions, please contact us:

mailto: molva.eurovis at gmail.com <mailto:molva.eurovis at gmail.com>?

?

Submission

************************************************************************

Please submit your short and full papers via PCS (Deadline: February 21,
2020):

https://new.precisionconference.com/(EuroVis & Eurographics 2020 MolVA
Workshop)??


Please follow the EG guidelines for writing the paper. You can find more
info here and templates below:

https://www.eurovis.org/submission-guidelines/

https://tinyurl.com/MolVA2020-zip?


Best regards,

???Jan By?ka, Michael Krone, Bjorn Sommer

???MolVA 2020 Organizing Committee

*
?

From jalemkul at vt.edu  Fri Jan 10 01:30:12 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Fri, 10 Jan 2020 00:30:12 -0000
Subject: [gmx-users] Index group for Backbone/C-alpha of specific
 stretch of residues
In-Reply-To: <CAOvdM4XkZY_ANmne9WRi1-Mva8GmdD_AycL0Uw=Lge8MU2qQMQ@mail.gmail.com>
References: <CAOvdM4W-5S2p8hKqGKy7-fsnbqz7Z0e4VBxHL+AwbA+zo7NPhg@mail.gmail.com>
	<CAOvdM4U-zTODkZSpHmvq2b87vgKx3f+yiGQbDcCKZrfYBuGW-A@mail.gmail.com>
	<922883ca-28a2-f6ca-9647-548baf78d43d@kth.se>
	<0e6f9056-c489-fd37-fdba-eea0a105783b@vt.edu>
	<CAOvdM4XkZY_ANmne9WRi1-Mva8GmdD_AycL0Uw=Lge8MU2qQMQ@mail.gmail.com>
Message-ID: <a546487e-80b2-d568-98bd-ab2c5653286d@vt.edu>



On 1/9/20 9:42 AM, Navneet Kumar wrote:
> Thank You, sir!
>
> What If I want to extend the residues like choose c-alpha of 150-200 &
> 60-70 in a single index group ?

3 & r 60-70 | 3 & r 150-200

Type "help" at the make_ndx prompt for examples of how to use the program.

-Justin

>
> On Wed, Jan 8, 2020 at 6:21 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 1/8/20 4:49 AM, Christian Blau wrote:
>>> Hi Navnett,
>>>
>>>
>>> gmx select will be your friend.
>>>
>>>
>>> At the bottom of
>>>
>>>
>> http://manual.gromacs.org/documentation/current/onlinehelp/selections.html
>>>
>>> you'll find some example commands. Something along the lines of
>>>
>>>    gmx select -select 'name CA and resid > 149 and resid < 211'
>>>
>>> should work.
>>>
>>>
>>> It's a very powerful syntax and I figured for me it was very much
>>> worth the effort reading through that documentation.
>>>
>> It's also simple in make_ndx:
>>
>> 3 & r 150-210
>>
>> Either way works. Whatever you find easier to use.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From xuyh1 at shanghaitech.edu.cn  Fri Jan 10 02:07:50 2020
From: xuyh1 at shanghaitech.edu.cn (=?gb2312?B?0OzS1Lvh?=)
Date: Fri, 10 Jan 2020 01:07:50 -0000
Subject: [gmx-users] Lipids running out of simulation box
In-Reply-To: <35810CB6446EC74FA538D5695A60C68E750B2479@DAGNODE9.shanghaitech.edu.cn>
References: <35810CB6446EC74FA538D5695A60C68E750B2479@DAGNODE9.shanghaitech.edu.cn>
Message-ID: <35810CB6446EC74FA538D5695A60C68E750B294F@DAGNODE9.shanghaitech.edu.cn>

Dear all,

I am simulating a lipid bilayer under dehydration (1:5 lipid/water). In order to compare it with the bilayer periodicity d of X-ray diffraction. As the paper suggests for dehydrated membrane,
https://www.researchgate.net/publication/292341967_Solvent-exposed_lipid_tail_protrusions_depend_on_lipid_membrane_composition_and_curvature
I built up a double-bilayer using packmol rather than solvate (to precisely control the number of water).
As the water layer is very thin, many DOPC run out of the simulation box.  Trjconv can surely repair the appearance, but I assume the bilayer periodicity (z1-z2) is longer accurate. 

So my questions:
(1) Is double bilayer a good system to obtain d?
(2) Does lipids out of box affect the calculation of d?
(3) If so, how to prevent it?  

Kind regards,
Yihui Xu
---
School of Physical Science and Technology at ShanghaiTech University
Shanghai, China


From navneetcdl at gmail.com  Fri Jan 10 05:57:37 2020
From: navneetcdl at gmail.com (Navneet Kumar)
Date: Fri, 10 Jan 2020 04:57:37 -0000
Subject: [gmx-users] Index group for Backbone/C-alpha of specific
 stretch of residues
In-Reply-To: <a546487e-80b2-d568-98bd-ab2c5653286d@vt.edu>
References: <CAOvdM4W-5S2p8hKqGKy7-fsnbqz7Z0e4VBxHL+AwbA+zo7NPhg@mail.gmail.com>
	<CAOvdM4U-zTODkZSpHmvq2b87vgKx3f+yiGQbDcCKZrfYBuGW-A@mail.gmail.com>
	<922883ca-28a2-f6ca-9647-548baf78d43d@kth.se>
	<0e6f9056-c489-fd37-fdba-eea0a105783b@vt.edu>
	<CAOvdM4XkZY_ANmne9WRi1-Mva8GmdD_AycL0Uw=Lge8MU2qQMQ@mail.gmail.com>
	<a546487e-80b2-d568-98bd-ab2c5653286d@vt.edu>
Message-ID: <CAOvdM4UZsHufwyQtmZFkOpVSiCPikiLDc-6sqTzeqYJ-kk-4tA@mail.gmail.com>

Thankyou!

On Fri, Jan 10, 2020 at 6:00 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/9/20 9:42 AM, Navneet Kumar wrote:
> > Thank You, sir!
> >
> > What If I want to extend the residues like choose c-alpha of 150-200 &
> > 60-70 in a single index group ?
>
> 3 & r 60-70 | 3 & r 150-200
>
> Type "help" at the make_ndx prompt for examples of how to use the program.
>
> -Justin
>
> >
> > On Wed, Jan 8, 2020 at 6:21 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >> On 1/8/20 4:49 AM, Christian Blau wrote:
> >>> Hi Navnett,
> >>>
> >>>
> >>> gmx select will be your friend.
> >>>
> >>>
> >>> At the bottom of
> >>>
> >>>
> >>
> http://manual.gromacs.org/documentation/current/onlinehelp/selections.html
> >>>
> >>> you'll find some example commands. Something along the lines of
> >>>
> >>>    gmx select -select 'name CA and resid > 149 and resid < 211'
> >>>
> >>> should work.
> >>>
> >>>
> >>> It's a very powerful syntax and I figured for me it was very much
> >>> worth the effort reading through that documentation.
> >>>
> >> It's also simple in make_ndx:
> >>
> >> 3 & r 150-210
> >>
> >> Either way works. Whatever you find easier to use.
> >>
> >> -Justin
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Office: 301 Fralin Hall
> >> Lab: 303 Engel Hall
> >>
> >> Virginia Tech Department of Biochemistry
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalemkul at vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==================================================
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >
> >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>


-- 






     Thanks & Regards
_______________________________________________________

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneetcdl at gmail.com  <navneetcdl at gmail.com>
<http://www.linkedin.com/in/navneet-kumar-74391814a/>
<http://facebook.com/xeon.singh> <http://instagram.com/snavneetkumar>

Please consider your environmental responsibility. Before printing this
e-mail message, ask yourself whether you really need a hard copy.

From aayattimg at bose.res.in  Fri Jan 10 07:03:29 2020
From: aayattimg at bose.res.in (aayattimg at bose.res.in)
Date: Fri, 10 Jan 2020 06:03:29 -0000
Subject: [gmx-users] gmx_topolbuild error
Message-ID: <48026.103.230.166.2.1578635136.squirrel@bose.res.in>

I am getting error in topolbuild:
Fatal error.
Source code file: readmol2.c, line: 693
Atom 1 (O5') has 2 connections when allowed 0
 I have used the command
./topolbuild -dir /home/aayatti/topolbuild1_2_1/dat/leap/parm -ff amber -n
tripos97
.mol2 file that I am using is as follows:
@<TRIPOS>MOLECULE
QCH
   30    31     1     0     1
SMALL
USER_CHARGES
@<TRIPOS>ATOM
  1 O5'        -1.938234    2.221639    0.669368 O         1 QCH      
-0.6458 ****
  2 H5T        -2.161090    3.085515    0.989879 H         1 QCH       
0.4497 ****
  3 O3'        -3.459429   -1.728789    0.016186 O         1 QCH      
-0.6852 ****
  4 H3T        -3.700920   -2.323917    0.713748 H         1 QCH       
0.4392 ****
  5 C1'        -0.662286   -0.787261   -0.296578 C         1 QCH       
0.3964 ****
  6 H1'        -0.605691   -1.741658   -0.791073 H         1 QCH       
0.0394 ****
  7 C2'        -1.435951   -0.850884    1.016075 C         1 QCH      
-0.0947 ****
  8 H2'1       -1.108767   -0.064159    1.683744 H         1 QCH       
0.0480 ****
  9 H2'2       -1.331556   -1.807305    1.511592 H         1 QCH       
0.0480 ****
 10 C3'        -2.859368   -0.575997    0.536996 C         1 QCH       
0.2991 ****
 11 H3'        -3.474441   -0.127033    1.307751 H         1 QCH       
0.0153 ****
 12 C4'        -2.644620    0.372686   -0.650794 C         1 QCH       
0.1743 ****
 13 H4'        -3.310149    0.087545   -1.452894 H         1 QCH       
0.0890 ****
 14 C5'        -2.828924    1.845500   -0.355885 C         1 QCH       
0.0150 ****
 15 H5'1       -2.633260    2.416008   -1.257986 H         1 QCH       
0.0776 ****
 16 H5'2       -3.858755    2.018514   -0.059368 H         1 QCH       
0.0776 ****
 17 O4'        -1.304632    0.148647   -1.085285 O         1 QCH      
-0.4154 ****
 18 N1          0.746765   -0.330172   -0.139522 N         1 QCH      
-0.0020 ****
 19 C6          1.037481    0.982281   -0.067547 C         1 QCH      
-0.1180 ****
 20 H6          0.189023    1.636860   -0.090671 H         1 QCH       
0.2766 ****
 21 C5          2.303418    1.459166    0.033557 C         1 QCH      
-0.2943 ****
 22 H5          2.501789    2.509565    0.085307 H         1 QCH       
0.1984 ****
 23 C4          3.355190    0.521532    0.053970 C         1 QCH       
0.4864 ****
 24 N4          4.624825    0.860634    0.131082 N         1 QCH      
-0.8725 ****
 25 H41         5.362632    0.189871    0.139293 H         1 QCH       
0.4651 ****
 26 H42         4.887551    1.821377    0.170549 H         1 QCH       
0.4651 ****
 27 N3          3.028239   -0.778715   -0.004253 N         1 QCH      
-0.2232 ****
 28 H3          3.730821   -1.491229    0.018101 H         1 QCH       
0.3215 ****
 29 C2          1.731998   -1.290150   -0.085103 C         1 QCH       
0.4517 ****
 30 O2          1.543842   -2.458176   -0.098679 O         1 QCH      
-0.4823 ****
@<TRIPOS>BOND
    1     1     2 1
    2     1    14 1
    3     3     4 1
    4     3    10 1
    5     5     6 1
    6     5     7 1
    7     5    17 1
    8     5    18 1
    9     7     8 1
   10     7     9 1
   11     7    10 1
   12    10    11 1
   13    10    12 1
   14    12    13 1
   15    12    14 1
   16    12    17 1
   17    14    15 1
   18    14    16 1
   19    18    19 1
   20    18    29 1
   21    19    20 1
   22    19    21 1
   23    21    22 1
   24    21    23 1
   25    23    24 1
   26    23    27 1
   27    24    25 1
   28    24    26 1
   29    27    28 1
   30    27    29 1
   31    29    30 1
@<TRIPOS>SUBSTRUCTURE
      1  QCH              1 ****               0 ****  ****




kindly suggest to debug the error.
Thanking you in advance.


From blau at kth.se  Fri Jan 10 08:54:25 2020
From: blau at kth.se (Christian Blau)
Date: Fri, 10 Jan 2020 07:54:25 -0000
Subject: [gmx-users] Replica exchange probabilities and extend simulation
In-Reply-To: <DB8PR10MB26498147F3CBFE59B8ACF839EA390@DB8PR10MB2649.EURPRD10.PROD.OUTLOOK.COM>
References: <DB8PR10MB26498147F3CBFE59B8ACF839EA390@DB8PR10MB2649.EURPRD10.PROD.OUTLOOK.COM>
Message-ID: <57b3bbc1-9874-0c5b-2d26-6f07cfd0c5f8@kth.se>

Hi Ahmed,


If you have a look into "Optimal temperature ladders in replica exchange simulations", available here:

https://www.sciencedirect.com/science/article/pii/S000926140900356X

you will see that your exchange probabilities should be a bit higher. Then again, you might have to set up a lot more 
simulations, which you can get around with more advanced protocols like solute tempering (REST). These methods are 
implemented in PLUMED for example.


If you want further insight, I suggest using

demux.pl md.log

It's a good sign if you see single replicas walking through the whole temperature range, it's a bad sign if you see that 
some replicas only stay close to a certain temperature.


Best,

Christian


On 2020-01-09 14:58, hind ahmed wrote:
> Dear All,
>
>   Are these probabilities good? and how can I extend the simulation of replica-exchange?
>
> Thanks
>
> Replica exchange statistics
> Repl  14999 attempts, 7500 odd, 7499 even
> Repl  average probabilities:
> Repl     0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31
> Repl      .03  .04  .04  .04  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .02  .02  .02  .01  .02  .02  .02  .02  .02
> Repl  number of exchanges:
> Repl     0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31
> Repl      259  263  270  330   62   57   63   58   65   67   71   74   89   87   88  103  100  103   98   98  114   93  132  127  149  111  117  126  129  124  145
> Repl  average number of exchanges:
> Repl     0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31
> Repl      .03  .04  .04  .04  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .02  .01  .02  .02  .02  .01  .02  .02  .02  .02  .02
>

From shanjayasinghe2011 at gmail.com  Fri Jan 10 08:55:49 2020
From: shanjayasinghe2011 at gmail.com (Shan Jayasinghe)
Date: Fri, 10 Jan 2020 07:55:49 -0000
Subject: [gmx-users] Make index command in gromacs
In-Reply-To: <46522240-0566-0c8e-b1d9-f7133b85bd52@kth.se>
References: <CAChmq0iqZVt=d0eYaQ6xERamDAds4_ZXtdnW=ks2b_zqNKYt3g@mail.gmail.com>
	<46522240-0566-0c8e-b1d9-f7133b85bd52@kth.se>
Message-ID: <CAChmq0gaXjNoe4GT8gAU0BmYTLEnBy-=xVnN4YGxverPpcXAiA@mail.gmail.com>

Dear Gromacs Users,

Thank you very much for your valuable answers.

On Wed, Jan 8, 2020 at 8:40 PM Christian Blau <blau at kth.se> wrote:

> Hi Shan,
>
>
> gmx select gives you many more options to do complex arithmetic with
> selections that might help you here.
>
>
> You can try using
>
> gmx select -select "SELECTION STING"
>
> you'll find lots of selection string examples at the bottom in here:
>
> http://manual.gromacs.org/documentation/current/onlinehelp/selections.html
>
>
>
> Best,
>
> Christian
>
>
> On 2020-01-07 23:33, Shan Jayasinghe wrote:
> > Dear Gromacs Users,
> >
> > In my simulations, I have different sizes of water droplets.  I need
> > indexes of water molecules in each droplet separately. I am trying to
> make
> > the  index file with gmx make_ndx, but I couldn't do it. Appreciate your
> > help regarding this matter.
> >
> > Thank you.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>


-- 
Best Regards
Shan Jayasinghe

From blau at kth.se  Fri Jan 10 08:56:36 2020
From: blau at kth.se (Christian Blau)
Date: Fri, 10 Jan 2020 07:56:36 -0000
Subject: [gmx-users] Visualize replica exchange
In-Reply-To: <DB8PR10MB26495E9BC7CDB127F3170533EA390@DB8PR10MB2649.EURPRD10.PROD.OUTLOOK.COM>
References: <DB8PR10MB26495E9BC7CDB127F3170533EA390@DB8PR10MB2649.EURPRD10.PROD.OUTLOOK.COM>
Message-ID: <9c949255-3453-56bf-082d-19df16b91404@kth.se>

Hi Ahmed,


I don't know about VMD, but you can try

./gromacs/scripts/demux.pl


Best,

Christian

On 2020-01-09 15:01, hind ahmed wrote:
> Dear All,
>
> How can I visualize replica exchange in VMD?
>
> Thanks

From byunjy0614 at gmail.com  Fri Jan 10 09:25:03 2020
From: byunjy0614 at gmail.com (=?utf-8?B?67OA7KeE7JiB?=)
Date: Fri, 10 Jan 2020 08:25:03 -0000
Subject: [gmx-users] Which content is in gmx wham -hist output file?
Message-ID: <79DD5359-AEB9-4AE8-A6F8-1138DDC94453@gmail.com>

Dear All,
I have tried to run umbrella sampling with GROMACS.
When I tried to analyze the umbrella sampling MD simulation result,  I used the module, gmx wham so that I got the result file named ?histo.xvg? .
What I wonder is what does columns mean except the 1st. column(I know the 1st. column is reaction coordinate.)
I think that roughly the other columns except the 1st. Columns mean the counts or probability for each reaction coordinate, but I don?t know what the columns suggested in detail.

Do you know what they are????

Thank you

From shakirashukoor1993 at gmail.com  Fri Jan 10 09:29:55 2020
From: shakirashukoor1993 at gmail.com (shakira shukoor)
Date: Fri, 10 Jan 2020 08:29:55 -0000
Subject: [gmx-users] Which content is in gmx wham -hist output file?
In-Reply-To: <79DD5359-AEB9-4AE8-A6F8-1138DDC94453@gmail.com>
References: <79DD5359-AEB9-4AE8-A6F8-1138DDC94453@gmail.com>
Message-ID: <CADV28mdJ1PMw-B6quN02ZH4pB0y_BRXup=j+BNjkx+yZ6-=O5A@mail.gmail.com>

The different columns indicates the counts or probability of different
binning distances or the windows you have considered in the simulation.

On Fri, Jan 10, 2020 at 1:55 PM ??? <byunjy0614 at gmail.com> wrote:

> Dear All,
> I have tried to run umbrella sampling with GROMACS.
> When I tried to analyze the umbrella sampling MD simulation result,  I
> used the module, gmx wham so that I got the result file named ?histo.xvg? .
> What I wonder is what does columns mean except the 1st. column(I know the
> 1st. column is reaction coordinate.)
> I think that roughly the other columns except the 1st. Columns mean the
> counts or probability for each reaction coordinate, but I don?t know what
> the columns suggested in detail.
>
> Do you know what they are????
>
> Thank you
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.



-- 
*Best Regards*

Shakkira E
PhD student INSPIRE Scholar
Department of Chemistry
sdmdlab.xyz
IIT Patna
Bihta
Patna 801106

From byunjy0614 at gmail.com  Fri Jan 10 09:43:07 2020
From: byunjy0614 at gmail.com (=?utf-8?B?67OA7KeE7JiB?=)
Date: Fri, 10 Jan 2020 08:43:07 -0000
Subject: [gmx-users] Which content is in gmx wham -hist output file?
In-Reply-To: <CADV28mdJ1PMw-B6quN02ZH4pB0y_BRXup=j+BNjkx+yZ6-=O5A@mail.gmail.com>
References: <79DD5359-AEB9-4AE8-A6F8-1138DDC94453@gmail.com>
	<CADV28mdJ1PMw-B6quN02ZH4pB0y_BRXup=j+BNjkx+yZ6-=O5A@mail.gmail.com>
Message-ID: <B0A51DA9-89F0-433C-9852-2AE935045111@gmail.com>

Each column has 0.1nm binning distance or the other distance length??


> 2020. 1. 10. ?? 5:28, shakira shukoor <shakirashukoor1993 at gmail.com> ??:
> 
> The different columns indicates the counts or probability of different
> binning distances or the windows you have considered in the simulation.
> 
> On Fri, Jan 10, 2020 at 1:55 PM ??? <byunjy0614 at gmail.com> wrote:
> 
>> Dear All,
>> I have tried to run umbrella sampling with GROMACS.
>> When I tried to analyze the umbrella sampling MD simulation result,  I
>> used the module, gmx wham so that I got the result file named ?histo.xvg? .
>> What I wonder is what does columns mean except the 1st. column(I know the
>> 1st. column is reaction coordinate.)
>> I think that roughly the other columns except the 1st. Columns mean the
>> counts or probability for each reaction coordinate, but I don?t know what
>> the columns suggested in detail.
>> 
>> Do you know what they are????
>> 
>> Thank you
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>> 
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
> 
> 
> 
> -- 
> *Best Regards*
> 
> Shakkira E
> PhD student INSPIRE Scholar
> Department of Chemistry
> sdmdlab.xyz
> IIT Patna
> Bihta
> Patna 801106
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.


From baswanth.oruganti at gmail.com  Fri Jan 10 09:51:13 2020
From: baswanth.oruganti at gmail.com (Baswanth Oruganti)
Date: Fri, 10 Jan 2020 08:51:13 -0000
Subject: [gmx-users] Protein breaking apart in implicit solvent MD
	simulations using GROMACS
Message-ID: <CALZ2dNw+ZAGeZAOWxcGK_baX87cvtQrOzANQ=ebL8Nj7uEzwUQ@mail.gmail.com>

Dear all,

I have been trying to perform implicit solvent MD simulations on a Kinase
protein. Gromacs is crashing with several LINCS warnings such as one shown
below. When I visualize output with vmd, I see that some atoms move very
large distances and finally protein is breaking apart.

Before the production MD run, I did energy minimization and a
position-restraint equilibration with a smaller time step than that of
production run. The starting configurations for the energy minimization are
taken from EDS sampling of a 50 ns trajectory run in explicit solvent.
Energy minimization output is also shown below.

I am also attaching the .mdp files I used for E minimization (em.mdp),
position-restraint equilibration (pr.mdp) and production MD run
(implicit.mdp). Could you suggest me ways to troubleshoot this issue?

Error:












* "Step 6907, time 6.907 (ps)  LINCS WARNING relative constraint deviation
after LINCS: rms 0.000588, max 0.013660 (between atoms 1581 and 1583) bonds
that rotated more than 30 degrees:  atom 1 atom 2  angle  previous,
current, constraint length    1591   1593   36.0    0.1346   0.1716
0.1345    1593   1594   42.9    0.0998   0.1386      0.0997    1593
1595   80.9    0.1437   0.2152      0.1430    1595   1596   87.0
0.1085   0.1613      0.1080    1595   1597  117.2    0.1549   0.1864
0.1538    1595   1615   68.1    0.1494   0.2074      0.1490" * Energy
Minimization output:
Steepest Descents converged to Fmax < 100 in 3065 steps
Potential Energy  = -1.7024426e+04
Maximum force     =  9.9019478e+01 on atom 3520
Norm of force     =  1.2291615e+01

Thanks & Regards,
Baswanth.

------------------------------

From alessandra.villa.biosim at gmail.com  Fri Jan 10 10:12:51 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Fri, 10 Jan 2020 09:12:51 -0000
Subject: [gmx-users] gmx_topolbuild error
In-Reply-To: <48026.103.230.166.2.1578635136.squirrel@bose.res.in>
References: <48026.103.230.166.2.1578635136.squirrel@bose.res.in>
Message-ID: <CANogp5ztTuUgvAGJWtcG5bJ4MyxwJdKirH82kHKxbrQNFpwd0Q@mail.gmail.com>

Hi,
I am not familiar with the software "topolbuild" (gmx topolbuild does not
exist), but I have noticed that  you are not using TRIPOS atom types in
your mol2 file.
Maybe that is a problem.
Best regards
Alessandra



On Fri, Jan 10, 2020 at 7:03 AM <aayattimg at bose.res.in> wrote:

> I am getting error in topolbuild:
> Fatal error.
> Source code file: readmol2.c, line: 693
> Atom 1 (O5') has 2 connections when allowed 0
>  I have used the command
> ./topolbuild -dir /home/aayatti/topolbuild1_2_1/dat/leap/parm -ff amber -n
> tripos97
> .mol2 file that I am using is as follows:
> @<TRIPOS>MOLECULE
> QCH
>    30    31     1     0     1
> SMALL
> USER_CHARGES
> @<TRIPOS>ATOM
>   1 O5'        -1.938234    2.221639    0.669368 O         1 QCH
> -0.6458 ****
>   2 H5T        -2.161090    3.085515    0.989879 H         1 QCH
> 0.4497 ****
>   3 O3'        -3.459429   -1.728789    0.016186 O         1 QCH
> -0.6852 ****
>   4 H3T        -3.700920   -2.323917    0.713748 H         1 QCH
> 0.4392 ****
>   5 C1'        -0.662286   -0.787261   -0.296578 C         1 QCH
> 0.3964 ****
>   6 H1'        -0.605691   -1.741658   -0.791073 H         1 QCH
> 0.0394 ****
>   7 C2'        -1.435951   -0.850884    1.016075 C         1 QCH
> -0.0947 ****
>   8 H2'1       -1.108767   -0.064159    1.683744 H         1 QCH
> 0.0480 ****
>   9 H2'2       -1.331556   -1.807305    1.511592 H         1 QCH
> 0.0480 ****
>  10 C3'        -2.859368   -0.575997    0.536996 C         1 QCH
> 0.2991 ****
>  11 H3'        -3.474441   -0.127033    1.307751 H         1 QCH
> 0.0153 ****
>  12 C4'        -2.644620    0.372686   -0.650794 C         1 QCH
> 0.1743 ****
>  13 H4'        -3.310149    0.087545   -1.452894 H         1 QCH
> 0.0890 ****
>  14 C5'        -2.828924    1.845500   -0.355885 C         1 QCH
> 0.0150 ****
>  15 H5'1       -2.633260    2.416008   -1.257986 H         1 QCH
> 0.0776 ****
>  16 H5'2       -3.858755    2.018514   -0.059368 H         1 QCH
> 0.0776 ****
>  17 O4'        -1.304632    0.148647   -1.085285 O         1 QCH
> -0.4154 ****
>  18 N1          0.746765   -0.330172   -0.139522 N         1 QCH
> -0.0020 ****
>  19 C6          1.037481    0.982281   -0.067547 C         1 QCH
> -0.1180 ****
>  20 H6          0.189023    1.636860   -0.090671 H         1 QCH
> 0.2766 ****
>  21 C5          2.303418    1.459166    0.033557 C         1 QCH
> -0.2943 ****
>  22 H5          2.501789    2.509565    0.085307 H         1 QCH
> 0.1984 ****
>  23 C4          3.355190    0.521532    0.053970 C         1 QCH
> 0.4864 ****
>  24 N4          4.624825    0.860634    0.131082 N         1 QCH
> -0.8725 ****
>  25 H41         5.362632    0.189871    0.139293 H         1 QCH
> 0.4651 ****
>  26 H42         4.887551    1.821377    0.170549 H         1 QCH
> 0.4651 ****
>  27 N3          3.028239   -0.778715   -0.004253 N         1 QCH
> -0.2232 ****
>  28 H3          3.730821   -1.491229    0.018101 H         1 QCH
> 0.3215 ****
>  29 C2          1.731998   -1.290150   -0.085103 C         1 QCH
> 0.4517 ****
>  30 O2          1.543842   -2.458176   -0.098679 O         1 QCH
> -0.4823 ****
> @<TRIPOS>BOND
>     1     1     2 1
>     2     1    14 1
>     3     3     4 1
>     4     3    10 1
>     5     5     6 1
>     6     5     7 1
>     7     5    17 1
>     8     5    18 1
>     9     7     8 1
>    10     7     9 1
>    11     7    10 1
>    12    10    11 1
>    13    10    12 1
>    14    12    13 1
>    15    12    14 1
>    16    12    17 1
>    17    14    15 1
>    18    14    16 1
>    19    18    19 1
>    20    18    29 1
>    21    19    20 1
>    22    19    21 1
>    23    21    22 1
>    24    21    23 1
>    25    23    24 1
>    26    23    27 1
>    27    24    25 1
>    28    24    26 1
>    29    27    28 1
>    30    27    29 1
>    31    29    30 1
> @<TRIPOS>SUBSTRUCTURE
>       1  QCH              1 ****               0 ****  ****
>
>
>
>
> kindly suggest to debug the error.
> Thanking you in advance.
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Fri Jan 10 10:12:51 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Fri, 10 Jan 2020 09:12:51 -0000
Subject: [gmx-users] gmx_topolbuild error
In-Reply-To: <48026.103.230.166.2.1578635136.squirrel@bose.res.in>
References: <48026.103.230.166.2.1578635136.squirrel@bose.res.in>
Message-ID: <CANogp5ztTuUgvAGJWtcG5bJ4MyxwJdKirH82kHKxbrQNFpwd0Q@mail.gmail.com>

Hi,
I am not familiar with the software "topolbuild" (gmx topolbuild does not
exist), but I have noticed that  you are not using TRIPOS atom types in
your mol2 file.
Maybe that is a problem.
Best regards
Alessandra



On Fri, Jan 10, 2020 at 7:03 AM <aayattimg at bose.res.in> wrote:

> I am getting error in topolbuild:
> Fatal error.
> Source code file: readmol2.c, line: 693
> Atom 1 (O5') has 2 connections when allowed 0
>  I have used the command
> ./topolbuild -dir /home/aayatti/topolbuild1_2_1/dat/leap/parm -ff amber -n
> tripos97
> .mol2 file that I am using is as follows:
> @<TRIPOS>MOLECULE
> QCH
>    30    31     1     0     1
> SMALL
> USER_CHARGES
> @<TRIPOS>ATOM
>   1 O5'        -1.938234    2.221639    0.669368 O         1 QCH
> -0.6458 ****
>   2 H5T        -2.161090    3.085515    0.989879 H         1 QCH
> 0.4497 ****
>   3 O3'        -3.459429   -1.728789    0.016186 O         1 QCH
> -0.6852 ****
>   4 H3T        -3.700920   -2.323917    0.713748 H         1 QCH
> 0.4392 ****
>   5 C1'        -0.662286   -0.787261   -0.296578 C         1 QCH
> 0.3964 ****
>   6 H1'        -0.605691   -1.741658   -0.791073 H         1 QCH
> 0.0394 ****
>   7 C2'        -1.435951   -0.850884    1.016075 C         1 QCH
> -0.0947 ****
>   8 H2'1       -1.108767   -0.064159    1.683744 H         1 QCH
> 0.0480 ****
>   9 H2'2       -1.331556   -1.807305    1.511592 H         1 QCH
> 0.0480 ****
>  10 C3'        -2.859368   -0.575997    0.536996 C         1 QCH
> 0.2991 ****
>  11 H3'        -3.474441   -0.127033    1.307751 H         1 QCH
> 0.0153 ****
>  12 C4'        -2.644620    0.372686   -0.650794 C         1 QCH
> 0.1743 ****
>  13 H4'        -3.310149    0.087545   -1.452894 H         1 QCH
> 0.0890 ****
>  14 C5'        -2.828924    1.845500   -0.355885 C         1 QCH
> 0.0150 ****
>  15 H5'1       -2.633260    2.416008   -1.257986 H         1 QCH
> 0.0776 ****
>  16 H5'2       -3.858755    2.018514   -0.059368 H         1 QCH
> 0.0776 ****
>  17 O4'        -1.304632    0.148647   -1.085285 O         1 QCH
> -0.4154 ****
>  18 N1          0.746765   -0.330172   -0.139522 N         1 QCH
> -0.0020 ****
>  19 C6          1.037481    0.982281   -0.067547 C         1 QCH
> -0.1180 ****
>  20 H6          0.189023    1.636860   -0.090671 H         1 QCH
> 0.2766 ****
>  21 C5          2.303418    1.459166    0.033557 C         1 QCH
> -0.2943 ****
>  22 H5          2.501789    2.509565    0.085307 H         1 QCH
> 0.1984 ****
>  23 C4          3.355190    0.521532    0.053970 C         1 QCH
> 0.4864 ****
>  24 N4          4.624825    0.860634    0.131082 N         1 QCH
> -0.8725 ****
>  25 H41         5.362632    0.189871    0.139293 H         1 QCH
> 0.4651 ****
>  26 H42         4.887551    1.821377    0.170549 H         1 QCH
> 0.4651 ****
>  27 N3          3.028239   -0.778715   -0.004253 N         1 QCH
> -0.2232 ****
>  28 H3          3.730821   -1.491229    0.018101 H         1 QCH
> 0.3215 ****
>  29 C2          1.731998   -1.290150   -0.085103 C         1 QCH
> 0.4517 ****
>  30 O2          1.543842   -2.458176   -0.098679 O         1 QCH
> -0.4823 ****
> @<TRIPOS>BOND
>     1     1     2 1
>     2     1    14 1
>     3     3     4 1
>     4     3    10 1
>     5     5     6 1
>     6     5     7 1
>     7     5    17 1
>     8     5    18 1
>     9     7     8 1
>    10     7     9 1
>    11     7    10 1
>    12    10    11 1
>    13    10    12 1
>    14    12    13 1
>    15    12    14 1
>    16    12    17 1
>    17    14    15 1
>    18    14    16 1
>    19    18    19 1
>    20    18    29 1
>    21    19    20 1
>    22    19    21 1
>    23    21    22 1
>    24    21    23 1
>    25    23    24 1
>    26    23    27 1
>    27    24    25 1
>    28    24    26 1
>    29    27    28 1
>    30    27    29 1
>    31    29    30 1
> @<TRIPOS>SUBSTRUCTURE
>       1  QCH              1 ****               0 ****  ****
>
>
>
>
> kindly suggest to debug the error.
> Thanking you in advance.
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From shakirashukoor1993 at gmail.com  Fri Jan 10 10:36:22 2020
From: shakirashukoor1993 at gmail.com (shakira shukoor)
Date: Fri, 10 Jan 2020 09:36:22 -0000
Subject: [gmx-users] Which content is in gmx wham -hist output file?
In-Reply-To: <B0A51DA9-89F0-433C-9852-2AE935045111@gmail.com>
References: <79DD5359-AEB9-4AE8-A6F8-1138DDC94453@gmail.com>
	<CADV28mdJ1PMw-B6quN02ZH4pB0y_BRXup=j+BNjkx+yZ6-=O5A@mail.gmail.com>
	<B0A51DA9-89F0-433C-9852-2AE935045111@gmail.com>
Message-ID: <CADV28mf4Ab9ZevSrVyGsjdVU6oqAD_n8kWJavO8suvXeYXN23g@mail.gmail.com>

That depends on your sampled positions which you will give as pull.xvg
files. And also there is -bins flag option in gmx wham where you can
mention the number of bins if you want to sample more.

On Fri, Jan 10, 2020 at 2:13 PM ??? <byunjy0614 at gmail.com> wrote:

> Each column has 0.1nm binning distance or the other distance length??
>
>
> > 2020. 1. 10. ?? 5:28, shakira shukoor <shakirashukoor1993 at gmail.com> ??:
> >
> > The different columns indicates the counts or probability of different
> > binning distances or the windows you have considered in the simulation.
> >
> > On Fri, Jan 10, 2020 at 1:55 PM ??? <byunjy0614 at gmail.com> wrote:
> >
> >> Dear All,
> >> I have tried to run umbrella sampling with GROMACS.
> >> When I tried to analyze the umbrella sampling MD simulation result,  I
> >> used the module, gmx wham so that I got the result file named
> ?histo.xvg? .
> >> What I wonder is what does columns mean except the 1st. column(I know
> the
> >> 1st. column is reaction coordinate.)
> >> I think that roughly the other columns except the 1st. Columns mean the
> >> counts or probability for each reaction coordinate, but I don?t know
> what
> >> the columns suggested in detail.
> >>
> >> Do you know what they are????
> >>
> >> Thank you
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >
> >
> >
> > --
> > *Best Regards*
> >
> > Shakkira E
> > PhD student INSPIRE Scholar
> > Department of Chemistry
> > sdmdlab.xyz
> > IIT Patna
> > Bihta
> > Patna 801106
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.



-- 
*Best Regards*

Shakkira E
PhD student INSPIRE Scholar
Department of Chemistry
sdmdlab.xyz
IIT Patna
Bihta
Patna 801106

From jmdamas at itqb.unl.pt  Fri Jan 10 10:47:23 2020
From: jmdamas at itqb.unl.pt (=?UTF-8?B?Sm/Do28gTS4gRGFtYXM=?=)
Date: Fri, 10 Jan 2020 09:47:23 -0000
Subject: [gmx-users] Building full GROMACS and mdrun only with MPI and GPU:
 FFTW and regression tests
Message-ID: <CAN8VxHzZQcQ8G-6PjVz0aRwMgYX8mQqTK5=xrLs2kO0G9cK8Og@mail.gmail.com>

Hi all,

I am trying to build GROMACS in a similar fashion to what is described in
section 2.3.5 of the manual (weblink
<http://manual.gromacs.org/documentation/2019.5/install-guide/index.html#testing-gromacs-for-correctness>),
i.e. a full build of GROMACS without any particular flags, and then a build
of mdrun only, with MPI and GPU enabled.

My first issue would be with the compilation of the FFT library, namely the
recommended FFTW through -DGMX_BUILD_OWN_FFTW=ON. I find that flag very
useful, but with a recipe as described in section 2.3.5, it would mean
compiling FFTW twice, which is a waste of time. Do you recommend for me to
compile FFTW separately on my own or is there a way/flag to pass the
compiled static library to the mdrun building step?

My second issue is with the regression tests. Using the procedure of
section 2.3.5, with a mdrun building recipe like this:

cmake3 .. \
       -DCMAKE_INSTALL_PREFIX=${SOFTWARE_INSTALL_PREFIX} \
       -DGMX_BUILD_OWN_FFTW=ON \
       -DGMX_DEFAULT_SUFFIX=OFF \
       -DGMX_BINARY_SUFFIX=_mpi \
       -DGMX_LIBS_SUFFIX=_mpi \
       -DGMX_MPI=ON \
       -DGMX_GPU=ON \
       -DGMX_BUILD_MDRUN_ONLY=ON
make -j ${NPROCS}
make install

there are issues with running `./gmxtest.pl all -np ${NPROCS} -mdrun
mdrun_mpi`. Since I am using the same install prefix for both building
steps, I am using the suffix flags stated, but then I need to fix
gmxtest.pl (namely
change the autosuffix variable from 1 to null) to make the tests run
(succesfully). Am I doing something wrong with the suffixes? I believe I
need them if I want to install on the same prefix.

Finally, is there a better way of doing this process to achieve the same
result (i.e. a full build of GROMACS without any particular flags, and then
a build of mdrun only, with MPI and GPU enabled)? In the case that section
is outdated.

Thank you in advance,
Jo?o

From mark.j.abraham at gmail.com  Fri Jan 10 16:00:48 2020
From: mark.j.abraham at gmail.com (Mark Abraham)
Date: Fri, 10 Jan 2020 15:00:48 -0000
Subject: [gmx-users] Building full GROMACS and mdrun only with MPI and
 GPU: FFTW and regression tests
In-Reply-To: <CAN8VxHzZQcQ8G-6PjVz0aRwMgYX8mQqTK5=xrLs2kO0G9cK8Og@mail.gmail.com>
References: <CAN8VxHzZQcQ8G-6PjVz0aRwMgYX8mQqTK5=xrLs2kO0G9cK8Og@mail.gmail.com>
Message-ID: <CAMNuMAQSxc8QdnY-EGcP2g8CTgLMjLdt=nDX5fLDL7i6YLawow@mail.gmail.com>

Hi,

On Fri, 10 Jan 2020 at 10:49, Jo?o M. Damas <jmdamas at itqb.unl.pt> wrote:

> Hi all,
>
> I am trying to build GROMACS in a similar fashion to what is described in
> section 2.3.5 of the manual (weblink
> <
> http://manual.gromacs.org/documentation/2019.5/install-guide/index.html#testing-gromacs-for-correctness
> >),
> i.e. a full build of GROMACS without any particular flags, and then a build
> of mdrun only, with MPI and GPU enabled.
>
> My first issue would be with the compilation of the FFT library, namely the
> recommended FFTW through -DGMX_BUILD_OWN_FFTW=ON. I find that flag very
> useful, but with a recipe as described in section 2.3.5, it would mean
> compiling FFTW twice, which is a waste of time. Do you recommend for me to
> compile FFTW separately on my own or is there a way/flag to pass the
> compiled static library to the mdrun building step?
>

No, the only way to do that is to have installed FFTW somewhere and have
both builds pick it up, e.g. through using cmake
-DCMAKE_PREFIX_PATH=/path/to/your/fftw. It's also not a lot of time, for
something you do rarely, so I would just ignore the inefficiency.


> My second issue is with the regression tests. Using the procedure of
> section 2.3.5, with a mdrun building recipe like this:
>
> cmake3 .. \
>        -DCMAKE_INSTALL_PREFIX=${SOFTWARE_INSTALL_PREFIX} \
>        -DGMX_BUILD_OWN_FFTW=ON \
>        -DGMX_DEFAULT_SUFFIX=OFF \
>        -DGMX_BINARY_SUFFIX=_mpi \
>        -DGMX_LIBS_SUFFIX=_mpi \
>

There's no need to do this - you're turning off the suffixing and then
doing the default behaviour yourself. It should work, but we don't try to
test it :-)

       -DGMX_MPI=ON \
>        -DGMX_GPU=ON \
>        -DGMX_BUILD_MDRUN_ONLY=ON
> make -j ${NPROCS}
> make install
>
> there are issues with running `./gmxtest.pl all -np ${NPROCS} -mdrun
> mdrun_mpi`. Since I am using the same install prefix for both building
> steps, I am using the suffix flags stated, but then I need to fix
> gmxtest.pl (namely
> change the autosuffix variable from 1 to null) to make the tests run
> (succesfully). Am I doing something wrong with the suffixes? I believe I
> need them if I want to install on the same prefix.
>

No. ./gmxtest.pl -nosuffix is useful for testing in the case you are doing,
and even though you're over-managing the suffixes, nothing's wrong.


> Finally, is there a better way of doing this process to achieve the same
> result (i.e. a full build of GROMACS without any particular flags, and then
> a build of mdrun only, with MPI and GPU enabled)? In the case that section
> is outdated.
>

This is the current procedure. There's currently no significant difference
between gmx_mpi mdrun and mdrun_mpi, except that one could reasonably want
to try harder to build the latter to link in a fully static way (which can
be worth a percent or two of performance).

Mark

Thank you in advance,
> Jo?o
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

From jmdamas at itqb.unl.pt  Fri Jan 10 16:30:28 2020
From: jmdamas at itqb.unl.pt (=?UTF-8?B?Sm/Do28gTS4gRGFtYXM=?=)
Date: Fri, 10 Jan 2020 15:30:28 -0000
Subject: [gmx-users] Building full GROMACS and mdrun only with MPI and
 GPU: FFTW and regression tests
In-Reply-To: <CAMNuMAQSxc8QdnY-EGcP2g8CTgLMjLdt=nDX5fLDL7i6YLawow@mail.gmail.com>
References: <CAN8VxHzZQcQ8G-6PjVz0aRwMgYX8mQqTK5=xrLs2kO0G9cK8Og@mail.gmail.com>
	<CAMNuMAQSxc8QdnY-EGcP2g8CTgLMjLdt=nDX5fLDL7i6YLawow@mail.gmail.com>
Message-ID: <CAN8VxHwCqw1QA=kZPk=GUbCBjR1KPQU1X53uL-Pn-7nDNB4-rw@mail.gmail.com>

On Fri, Jan 10, 2020 at 4:01 PM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> On Fri, 10 Jan 2020 at 10:49, Jo?o M. Damas <jmdamas at itqb.unl.pt> wrote:
>
> > Hi all,
> >
> > I am trying to build GROMACS in a similar fashion to what is described in
> > section 2.3.5 of the manual (weblink
> > <
> >
> http://manual.gromacs.org/documentation/2019.5/install-guide/index.html#testing-gromacs-for-correctness
> > >),
> > i.e. a full build of GROMACS without any particular flags, and then a
> build
> > of mdrun only, with MPI and GPU enabled.
> >
> > My first issue would be with the compilation of the FFT library, namely
> the
> > recommended FFTW through -DGMX_BUILD_OWN_FFTW=ON. I find that flag very
> > useful, but with a recipe as described in section 2.3.5, it would mean
> > compiling FFTW twice, which is a waste of time. Do you recommend for me
> to
> > compile FFTW separately on my own or is there a way/flag to pass the
> > compiled static library to the mdrun building step?
> >
>
> No, the only way to do that is to have installed FFTW somewhere and have
> both builds pick it up, e.g. through using cmake
> -DCMAKE_PREFIX_PATH=/path/to/your/fftw. It's also not a lot of time, for
> something you do rarely, so I would just ignore the inefficiency.
>
Thanks, that's what I thought. I'll see which of the two options is the
best for my case.

>
>
> > My second issue is with the regression tests. Using the procedure of
> > section 2.3.5, with a mdrun building recipe like this:
> >
> > cmake3 .. \
> >        -DCMAKE_INSTALL_PREFIX=${SOFTWARE_INSTALL_PREFIX} \
> >        -DGMX_BUILD_OWN_FFTW=ON \
> >        -DGMX_DEFAULT_SUFFIX=OFF \
> >        -DGMX_BINARY_SUFFIX=_mpi \
> >        -DGMX_LIBS_SUFFIX=_mpi \
> >
>
> There's no need to do this - you're turning off the suffixing and then
> doing the default behaviour yourself. It should work, but we don't try to
> test it :-)
>
Oh, a bit of over-engineering from my part, I see ?. I didn't actually
test that the -DGMX_MPI=ON changed the default suffix. Thanks for the
feedback.

>
>        -DGMX_MPI=ON \
> >        -DGMX_GPU=ON \
> >        -DGMX_BUILD_MDRUN_ONLY=ON
> > make -j ${NPROCS}
> > make install
> >
> > there are issues with running `./gmxtest.pl all -np ${NPROCS} -mdrun
> > mdrun_mpi`. Since I am using the same install prefix for both building
> > steps, I am using the suffix flags stated, but then I need to fix
> > gmxtest.pl (namely
> > change the autosuffix variable from 1 to null) to make the tests run
> > (succesfully). Am I doing something wrong with the suffixes? I believe I
> > need them if I want to install on the same prefix.
> >
>
> No. ./gmxtest.pl -nosuffix is useful for testing in the case you are
> doing,
> and even though you're over-managing the suffixes, nothing's wrong.
>
I guess that's the flag I was looking for! I'll try it. Thanks.

>
>
> > Finally, is there a better way of doing this process to achieve the same
> > result (i.e. a full build of GROMACS without any particular flags, and
> then
> > a build of mdrun only, with MPI and GPU enabled)? In the case that
> section
> > is outdated.
> >
>
> This is the current procedure. There's currently no significant difference
> between gmx_mpi mdrun and mdrun_mpi, except that one could reasonably want
> to try harder to build the latter to link in a fully static way (which can
> be worth a percent or two of performance).
>
Thanks for the extra input on this matter, I appreciate it.

>
> Mark
>
> Thank you in advance,
> > Jo?o
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.



-- 
Jo?o M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613

From b.mijiddorj at gmail.com  Fri Jan 10 16:55:36 2020
From: b.mijiddorj at gmail.com (Mijiddorj B)
Date: Fri, 10 Jan 2020 15:55:36 -0000
Subject: [gmx-users] Vibrational spectra of amide I using gromacs
In-Reply-To: <mailman.497.1578533652.1966.gromacs.org_gmx-users@maillist.sys.kth.se>
References: <mailman.497.1578533652.1966.gromacs.org_gmx-users@maillist.sys.kth.se>
Message-ID: <CABgRApv-9wrniSu1H0jj_Nii0Lb5GK9XiDhaqKMvTNukPP0YKw@mail.gmail.com>

 Dear Andre,

Thank you very much for your kind responses.
According to your suggestion, I calculated the bond length as a function of
time. The auto-correlation function was generated by gmx analyze. Then, I
used the xmgrace for the Fourier transform of the Auto-correlation function.
Is the workflow right? The result data does not look like some spectra. How
can I convert it into vibrational spectra and how can I adjust the unit?
If possible, please advise me?
Thank you again for your time.

Best regards,

Mijiddorj


> ------------------------------
>
> Message: 6
> Date: Wed, 8 Jan 2020 22:33:56 -0300
> From: Andr? Farias de Moura <moura at ufscar.br>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Vibrational spectra of amide I using gromacs
> Message-ID:
>         <
> CAKTwKgrecyH10WMA+Sw_86rHyoP9c6k2XsPknvYoEwiUfkyL1g at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear Mijiddorj,
>
> It is a matter of taste, but I like to use xmgrace for that kind of
> analysis.
>
> The GROMACS tool gmx analyze can do that for you:
> http://manual.gromacs.org/documentation/5.1/onlinehelp/gmx-analyze.html
>
> Andre
>
> On Wed, Jan 8, 2020 at 9:18 PM Mijiddorj B <b.mijiddorj at gmail.com> wrote:
>
> > Dear Andre
> >
> > Thank you very much for your quick response.
> > I am very new for this type of analysis, and I would like to ask
> further. I
> > am sorry for that. Is there any good software?
> > If you have any experience, please suggest me some useful software for
> the
> > time series correlation and the Fourier transformation.
> >
> > Best regards,
> >
> > Mijiddorj
> >
> > Should be doable using any standard spreadsheet:
> > >
> > > (1) save the bond lengths along the simulation for the bond of interest
> > >
> > > (2) compute the time correlation function for these bond lengths (the
> > > autocorrelation function for this time series)
> > >
> > > (3) compute the Fourier transform of the time correlation function
> > >
> > > Andre
> > >
> > > On Wed, Jan 8, 2020 at 11:37 AM Mijiddorj B <b.mijiddorj at gmail.com>
> > wrote:
> > >
> > > > Dear gmx users,
> > > >
> > > > Hello, I would like to ask vibrational spectra of amide of specific
> > > > amino acids. Is it possible to analyze from classic MD calculations
> of
> > > > gromacs?
> > > > Or
> > > >
> > > > Is there any software that is compatible with gmx trajectories  to
> > > > calculate the spectra?
> > > >
> > > > Best regards,
> > > >
> > > > Mijiddorj
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-request at gromacs.org.
> > > >
> > >
> > >
> > > --
> > > _____________
> > >
> > > Prof. Dr. Andr? Farias de Moura
> > > Department of Chemistry
> > > Federal University of S?o Carlos
> > > S?o Carlos - Brazil
> > > phone: +55-16-3351-8090
> > >
> > >
> > > ------------------------------
> > >
> > >
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> --
> _____________
>
> Prof. Dr. Andr? Farias de Moura
> Department of Chemistry
> Federal University of S?o Carlos
> S?o Carlos - Brazil
> phone: +55-16-3351-8090
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 189, Issue 19
> ******************************************************
>

From lvqingjiejie at 163.com  Fri Jan 10 17:03:08 2020
From: lvqingjiejie at 163.com (Qing Lv)
Date: Fri, 10 Jan 2020 16:03:08 -0000
Subject: [gmx-users] Is minimization and equilibration needed for umbrella
	sampling?
In-Reply-To: <CABgRApv-9wrniSu1H0jj_Nii0Lb5GK9XiDhaqKMvTNukPP0YKw@mail.gmail.com>
References: <mailman.497.1578533652.1966.gromacs.org_gmx-users@maillist.sys.kth.se>
	<CABgRApv-9wrniSu1H0jj_Nii0Lb5GK9XiDhaqKMvTNukPP0YKw@mail.gmail.com>
Message-ID: <4a04883d.c54a.16f90318a6a.Coremail.lvqingjiejie@163.com>

Dear Colleagues,


I am doing a QM/MM umbrella sampling to calculate the PMF of an enzymatic reaction. The initial coordinates (with solvents and ions) for each sampling window were extracted from previous trajectories. The reaction coordinate (bond length difference) of each initial frame was closed to the center of the window. So, need I do energy-minimization and equilibration for each window? Since each initial conformation has no bad clashes (actually they can run MD well without minimizations) and is closed to the window center, I cannot understand why minimization and equilibration are still needed (as a lot of references do so).


Thanks,
Qing

From alfredo at ices.utexas.edu  Fri Jan 10 21:00:49 2020
From: alfredo at ices.utexas.edu (Cardenas, Alfredo E)
Date: Fri, 10 Jan 2020 20:00:49 -0000
Subject: [gmx-users] Need help with installation of Gromacs-2019.3 with
 Intell compilers
Message-ID: <BN8PR06MB6001DE58F72E8605FC86A805EB380@BN8PR06MB6001.namprd06.prod.outlook.com>

Hi Roland and others gmx-users,
I am also getting a similar compilation error regarding pullutil.cpp:

icpc: error #10106: Fatal error in /opt/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom, terminated by floating point exception
compilation aborted for /home1/01247/alfredo/Software/gromacs-2019.4/src/gromacs/pulling/pullutil.cpp (code 1)
make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
make: *** [all] Error 2

using optimization for AVX512. I saw this post where you suggested a work-around adding "#pragma intel optimization_level 2" in front of pull_calc_coms. I see the line in pullutil.cpp:

void pull_calc_coms(const t_commrec *cr,
                    pull_t *pull,
                    const t_mdatoms *md,
                    t_pbc *pbc,
                    double t,
                    const rvec x[], rvec *xp)
{

I tried putting the pragma before void and it gave me a bunch of errors. Where exactly should it be added?
Thanks,

Alfredo

From roland.schulz at intel.com  Fri Jan 10 21:13:55 2020
From: roland.schulz at intel.com (Schulz, Roland)
Date: Fri, 10 Jan 2020 20:13:55 -0000
Subject: [gmx-users] Need help with installation of Gromacs-2019.3 with
 Intell compilers
In-Reply-To: <BN8PR06MB6001DE58F72E8605FC86A805EB380@BN8PR06MB6001.namprd06.prod.outlook.com>
References: <BN8PR06MB6001DE58F72E8605FC86A805EB380@BN8PR06MB6001.namprd06.prod.outlook.com>
Message-ID: <BYAPR11MB2581B470E0B9CB98F4DB7432E0380@BYAPR11MB2581.namprd11.prod.outlook.com>

Hi,

It needs to be on its own line prior to the void.
What will be in next version of GROMACS (2019.6 and 2020.1) is:
https://gerrit.gromacs.org/c/gromacs/+/15218/4/src/gromacs/pulling/pullutil.cpp

You don't need the #ifdef/#endif if you only care about compiling with ICC.

Roland

> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of
> Cardenas, Alfredo E
> Sent: Friday, January 10, 2020 12:00 PM
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Need help with installation of Gromacs-2019.3 with
> Intell compilers
> 
> Hi Roland and others gmx-users,
> I am also getting a similar compilation error regarding pullutil.cpp:
> 
> icpc: error #10106: Fatal error in
> /opt/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom,
> terminated by floating point exception compilation aborted for
> /home1/01247/alfredo/Software/gromacs-
> 2019.4/src/gromacs/pulling/pullutil.cpp (code 1)
> make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o]
> Error 1
> make[2]: *** Waiting for unfinished jobs....
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> make: *** [all] Error 2
> 
> using optimization for AVX512. I saw this post where you suggested a work-
> around adding "#pragma intel optimization_level 2" in front of
> pull_calc_coms. I see the line in pullutil.cpp:
> 
> void pull_calc_coms(const t_commrec *cr,
>                     pull_t *pull,
>                     const t_mdatoms *md,
>                     t_pbc *pbc,
>                     double t,
>                     const rvec x[], rvec *xp) {
> 
> I tried putting the pragma before void and it gave me a bunch of errors.
> Where exactly should it be added?
> Thanks,
> 
> Alfredo
> --
> Gromacs Users mailing list
> 
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
> a mail to gmx-users-request at gromacs.org.

From roland.schulz at intel.com  Fri Jan 10 21:15:00 2020
From: roland.schulz at intel.com (Schulz, Roland)
Date: Fri, 10 Jan 2020 20:15:00 -0000
Subject: [gmx-users] Need help with installation of Gromacs-2019.3 with
 Intell compilers
In-Reply-To: <BN8PR06MB6001DE58F72E8605FC86A805EB380@BN8PR06MB6001.namprd06.prod.outlook.com>
References: <BN8PR06MB6001DE58F72E8605FC86A805EB380@BN8PR06MB6001.namprd06.prod.outlook.com>
Message-ID: <BYAPR11MB2581B470E0B9CB98F4DB7432E0380@BYAPR11MB2581.namprd11.prod.outlook.com>

Hi,

It needs to be on its own line prior to the void.
What will be in next version of GROMACS (2019.6 and 2020.1) is:
https://gerrit.gromacs.org/c/gromacs/+/15218/4/src/gromacs/pulling/pullutil.cpp

You don't need the #ifdef/#endif if you only care about compiling with ICC.

Roland

> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of
> Cardenas, Alfredo E
> Sent: Friday, January 10, 2020 12:00 PM
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Need help with installation of Gromacs-2019.3 with
> Intell compilers
> 
> Hi Roland and others gmx-users,
> I am also getting a similar compilation error regarding pullutil.cpp:
> 
> icpc: error #10106: Fatal error in
> /opt/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom,
> terminated by floating point exception compilation aborted for
> /home1/01247/alfredo/Software/gromacs-
> 2019.4/src/gromacs/pulling/pullutil.cpp (code 1)
> make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o]
> Error 1
> make[2]: *** Waiting for unfinished jobs....
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> make: *** [all] Error 2
> 
> using optimization for AVX512. I saw this post where you suggested a work-
> around adding "#pragma intel optimization_level 2" in front of
> pull_calc_coms. I see the line in pullutil.cpp:
> 
> void pull_calc_coms(const t_commrec *cr,
>                     pull_t *pull,
>                     const t_mdatoms *md,
>                     t_pbc *pbc,
>                     double t,
>                     const rvec x[], rvec *xp) {
> 
> I tried putting the pragma before void and it gave me a bunch of errors.
> Where exactly should it be added?
> Thanks,
> 
> Alfredo
> --
> Gromacs Users mailing list
> 
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
> a mail to gmx-users-request at gromacs.org.

From palusoori at gmail.com  Fri Jan 10 21:20:10 2020
From: palusoori at gmail.com (Seera Suryanarayana)
Date: Fri, 10 Jan 2020 20:20:10 -0000
Subject: [gmx-users] How to find free energy barrier from FEL which
	generated from dPCA?
Message-ID: <CAAr94NN6OOhK4tR1D3djsRrCM3NzDq-YWTFLjWAEDn1t8tQh7A@mail.gmail.com>

Dear Gromacs users,
I have generated the FEL from dPCA of 20 residues length of peptide. I
check the fel.txt file which was used for the FEL generation in mathmatica.
I was not able to find the energy barriers from the FEL. I request you to
guide to how to find the free energy barriers from this FEL.

Thanks in

Surya
Graduate student
India.

From sundi6170 at gmail.com  Sat Jan 11 18:22:24 2020
From: sundi6170 at gmail.com (Sundari)
Date: Sat, 11 Jan 2020 17:22:24 -0000
Subject: [gmx-users] Query regarding do_dssp program
Message-ID: <CACgG5G_W98HHjQOVfcExjW09-4-93XRCChf5n8Hk6hYsY-XP4g@mail.gmail.com>

Dear Gromacs Users,

I have a big query regarding the "do_dssp" tool of gromacs-5.1.2.
Whenever I calculate the protein secondary structure by "gmx do_dssp" , it
shows a significant amount of beta sheet structures. But when I load the
same trajectory file in VMD for visualization of the secondary structure it
does not show any beta-sheet structures.

Please, anyone, clarify the issue.

Thank you in advance,

From aa.hind at hotmail.com  Sun Jan 12 23:02:06 2020
From: aa.hind at hotmail.com (hind ahmed)
Date: Sun, 12 Jan 2020 22:02:06 -0000
Subject: [gmx-users] solute tempering (REST2)
Message-ID: <DB8PR10MB2649D76668D34899D1E14ABAEA3A0@DB8PR10MB2649.EURPRD10.PROD.OUTLOOK.COM>

Dear All, 
Is there a tutorial for solute tempering (REST2) in gromacs or any clear guide to apply this method? 

Regards, 

Thank you 

Sent from my Huawei tablet

From pragati2325 at gmail.com  Mon Jan 13 08:42:44 2020
From: pragati2325 at gmail.com (Pragati Sharma)
Date: Mon, 13 Jan 2020 07:42:44 -0000
Subject: [gmx-users] Cut off (1.2 -1.5 nm) with OPLS forcefield
Message-ID: <CAMpF9Q2f96D=qwQ0nFVKm_4nm+1QTXep8bRTb8A9xwGW8SdJ6A@mail.gmail.com>

Hello all,

I am simulating a polymeric system using OPLS-AA forcefield.
I can see a considerable change in density while changing the cut off from
1.2 to 1.5 nm

cut off              Density                          Experimental density
1.2                    895 kg/m3                        910-920 kg/m3
1.5                    910 kg/m3


Should I change my cut off to 1.5 as it is giving me more accurate density,
OR I can't do it because OPLS-AA is parameterized with cut-off 1.0 nm.

Thanks

From alessandra.villa.biosim at gmail.com  Mon Jan 13 09:06:50 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Mon, 13 Jan 2020 08:06:50 -0000
Subject: [gmx-users] Query regarding do_dssp program
In-Reply-To: <CACgG5G_W98HHjQOVfcExjW09-4-93XRCChf5n8Hk6hYsY-XP4g@mail.gmail.com>
References: <CACgG5G_W98HHjQOVfcExjW09-4-93XRCChf5n8Hk6hYsY-XP4g@mail.gmail.com>
Message-ID: <CANogp5yG74V8SU9o6h4q4NT3P7=vc7r29fXo9PTGym_w5uMS-w@mail.gmail.com>

Hi,
VMD and dssp  may use a slightly different criteria to  define a beta
sheet.
First I will check in literature if the criteria are the same.
In some case, it occur that the  the atom types (e.i H) are not properly
recognized by the software,
and thus secondary structure element can not be determined.
Best regards
Alessandra



On Sat, Jan 11, 2020 at 6:23 PM Sundari <sundi6170 at gmail.com> wrote:

> Dear Gromacs Users,
>
> I have a big query regarding the "do_dssp" tool of gromacs-5.1.2.
> Whenever I calculate the protein secondary structure by "gmx do_dssp" , it
> shows a significant amount of beta sheet structures. But when I load the
> same trajectory file in VMD for visualization of the secondary structure it
> does not show any beta-sheet structures.
>
> Please, anyone, clarify the issue.
>
> Thank you in advance,
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Mon Jan 13 09:06:50 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Mon, 13 Jan 2020 08:06:50 -0000
Subject: [gmx-users] Query regarding do_dssp program
In-Reply-To: <CACgG5G_W98HHjQOVfcExjW09-4-93XRCChf5n8Hk6hYsY-XP4g@mail.gmail.com>
References: <CACgG5G_W98HHjQOVfcExjW09-4-93XRCChf5n8Hk6hYsY-XP4g@mail.gmail.com>
Message-ID: <CANogp5yG74V8SU9o6h4q4NT3P7=vc7r29fXo9PTGym_w5uMS-w@mail.gmail.com>

Hi,
VMD and dssp  may use a slightly different criteria to  define a beta
sheet.
First I will check in literature if the criteria are the same.
In some case, it occur that the  the atom types (e.i H) are not properly
recognized by the software,
and thus secondary structure element can not be determined.
Best regards
Alessandra



On Sat, Jan 11, 2020 at 6:23 PM Sundari <sundi6170 at gmail.com> wrote:

> Dear Gromacs Users,
>
> I have a big query regarding the "do_dssp" tool of gromacs-5.1.2.
> Whenever I calculate the protein secondary structure by "gmx do_dssp" , it
> shows a significant amount of beta sheet structures. But when I load the
> same trajectory file in VMD for visualization of the secondary structure it
> does not show any beta-sheet structures.
>
> Please, anyone, clarify the issue.
>
> Thank you in advance,
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Mon Jan 13 09:22:09 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Mon, 13 Jan 2020 08:22:09 -0000
Subject: [gmx-users] Cut off (1.2 -1.5 nm) with OPLS forcefield
In-Reply-To: <CAMpF9Q2f96D=qwQ0nFVKm_4nm+1QTXep8bRTb8A9xwGW8SdJ6A@mail.gmail.com>
References: <CAMpF9Q2f96D=qwQ0nFVKm_4nm+1QTXep8bRTb8A9xwGW8SdJ6A@mail.gmail.com>
Message-ID: <CANogp5xR26Q=Wf_7WqwAuc-bBgeHbdNFuJo75PEZyONh1qhE0A@mail.gmail.com>

Hi,
A general criteria is to apply the short and long range interaction setting
used in the parametization procedure.
Each force field has its own parameterization strategy. Among other that
guarantees  parameters consistency and results reproducibility.
Another story is if you are performing your own parameterization (of your
own force field).
Best regards
Alessandra

On Mon, Jan 13, 2020 at 8:42 AM Pragati Sharma <pragati2325 at gmail.com>
wrote:

> Hello all,
>
> I am simulating a polymeric system using OPLS-AA forcefield.
> I can see a considerable change in density while changing the cut off from
> 1.2 to 1.5 nm
>
> cut off              Density                          Experimental density
> 1.2                    895 kg/m3                        910-920 kg/m3
> 1.5                    910 kg/m3
>
>
> Should I change my cut off to 1.5 as it is giving me more accurate density,
> OR I can't do it because OPLS-AA is parameterized with cut-off 1.0 nm.
>
> Thanks
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Mon Jan 13 09:22:09 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Mon, 13 Jan 2020 08:22:09 -0000
Subject: [gmx-users] Cut off (1.2 -1.5 nm) with OPLS forcefield
In-Reply-To: <CAMpF9Q2f96D=qwQ0nFVKm_4nm+1QTXep8bRTb8A9xwGW8SdJ6A@mail.gmail.com>
References: <CAMpF9Q2f96D=qwQ0nFVKm_4nm+1QTXep8bRTb8A9xwGW8SdJ6A@mail.gmail.com>
Message-ID: <CANogp5xR26Q=Wf_7WqwAuc-bBgeHbdNFuJo75PEZyONh1qhE0A@mail.gmail.com>

Hi,
A general criteria is to apply the short and long range interaction setting
used in the parametization procedure.
Each force field has its own parameterization strategy. Among other that
guarantees  parameters consistency and results reproducibility.
Another story is if you are performing your own parameterization (of your
own force field).
Best regards
Alessandra

On Mon, Jan 13, 2020 at 8:42 AM Pragati Sharma <pragati2325 at gmail.com>
wrote:

> Hello all,
>
> I am simulating a polymeric system using OPLS-AA forcefield.
> I can see a considerable change in density while changing the cut off from
> 1.2 to 1.5 nm
>
> cut off              Density                          Experimental density
> 1.2                    895 kg/m3                        910-920 kg/m3
> 1.5                    910 kg/m3
>
>
> Should I change my cut off to 1.5 as it is giving me more accurate density,
> OR I can't do it because OPLS-AA is parameterized with cut-off 1.0 nm.
>
> Thanks
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From lalehan.ozalp at gmail.com  Mon Jan 13 11:32:50 2020
From: lalehan.ozalp at gmail.com (Lalehan Ozalp)
Date: Mon, 13 Jan 2020 10:32:50 -0000
Subject: [gmx-users] cannot load the xtc file (without PBC) to VMD
Message-ID: <CAKpt5Pe_zAOZiK18s3V_tzGiHZ3mFkK2e7dfD=7SsocgWYk6rw@mail.gmail.com>

Dear all, I have a question regarding loading .xtc file (with no periodic
boundary conditions) to VMD which I generated before. To this end, I had
used the command:
trjconv -f md_0_10.xtc -s md_30.tpr -n index.ndx -o noPBC.xtc -pbc mol -ur
compact -center
and selected *protein* for centering, and *system* for output.
However, when I load my corresponding gro file to VMD, and then loading the
xtc file above, the following error occurs:

ERROR) BaseMolecule: attempt to init atoms while structure building in
progress!
ERROR) Invalid number of atoms in file: 132259
Info) Using plugin xtc for coordinates from file
/home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc
ERROR) Incorrect number of atoms (132259) in
ERROR) coordinate file /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc
ERROR) Mismatch between existing molecule or structure file atom count and
coordinate or trajectory file atom count.
Info) Finished with coordinate file
/home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc.

This is especially strange since I carried out the same procedure several
times before. Additionally, I have a parallel system (with an isoenzyme of
the enzyme used here, with the same cofactor and the same ligand) and the
same steps worked perfectly. As a side note, this happens when I load xtc
file without PBC, while does not happen when I load xtc file in the
presence of PBC.

Thank you so much in advance!
Lalehan

From sundi6170 at gmail.com  Mon Jan 13 13:28:05 2020
From: sundi6170 at gmail.com (Sundari)
Date: Mon, 13 Jan 2020 12:28:05 -0000
Subject: [gmx-users] Query regarding do_dssp program
In-Reply-To: <CANogp5yG74V8SU9o6h4q4NT3P7=vc7r29fXo9PTGym_w5uMS-w@mail.gmail.com>
References: <CACgG5G_W98HHjQOVfcExjW09-4-93XRCChf5n8Hk6hYsY-XP4g@mail.gmail.com>
	<CANogp5yG74V8SU9o6h4q4NT3P7=vc7r29fXo9PTGym_w5uMS-w@mail.gmail.com>
Message-ID: <CACgG5G-upuHz8NV9ggCZo08eyzdYXm6n9SYt=daVTw5Y9z2Tug@mail.gmail.com>

Hello Dear,

Actually I was thinking the same i.e. gromacs use "dssp" criteria and vmd
use "stride" algorithm for secondary structure determination.
But the expected error in the two algorithms should not be more than 5%
according to the literature. Here, In my case, the structure contains a lot
of beta-sheets by dssp and that sequence in vmd is showing 5-helix instead
of beta-sheets. I am in a confusion now because I want the snapshots of the
structures obtained by gromacs dssp.

Can you please suggest which algorithm should I use for 2ndary structure or
there is any way to animate secondary structure in vmd according to dssp
algorithm.

Best regards,
Sundari

On Mon, Jan 13, 2020 at 1:37 PM Alessandra Villa <
alessandra.villa.biosim at gmail.com> wrote:

> Hi,
> VMD and dssp  may use a slightly different criteria to  define a beta
> sheet.
> First I will check in literature if the criteria are the same.
> In some case, it occur that the  the atom types (e.i H) are not properly
> recognized by the software,
> and thus secondary structure element can not be determined.
> Best regards
> Alessandra
>
>
>
> On Sat, Jan 11, 2020 at 6:23 PM Sundari <sundi6170 at gmail.com> wrote:
>
> > Dear Gromacs Users,
> >
> > I have a big query regarding the "do_dssp" tool of gromacs-5.1.2.
> > Whenever I calculate the protein secondary structure by "gmx do_dssp" ,
> it
> > shows a significant amount of beta sheet structures. But when I load the
> > same trajectory file in VMD for visualization of the secondary structure
> it
> > does not show any beta-sheet structures.
> >
> > Please, anyone, clarify the issue.
> >
> > Thank you in advance,
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From jalemkul at vt.edu  Mon Jan 13 14:29:38 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Mon, 13 Jan 2020 13:29:38 -0000
Subject: [gmx-users] Is minimization and equilibration needed for
 umbrella sampling?
In-Reply-To: <4a04883d.c54a.16f90318a6a.Coremail.lvqingjiejie@163.com>
References: <mailman.497.1578533652.1966.gromacs.org_gmx-users@maillist.sys.kth.se>
	<CABgRApv-9wrniSu1H0jj_Nii0Lb5GK9XiDhaqKMvTNukPP0YKw@mail.gmail.com>
	<4a04883d.c54a.16f90318a6a.Coremail.lvqingjiejie@163.com>
Message-ID: <79319b78-b288-e65b-151c-0269521d7b50@vt.edu>



On 1/10/20 11:02 AM, Qing Lv wrote:
> Dear Colleagues,
>
>
> I am doing a QM/MM umbrella sampling to calculate the PMF of an enzymatic reaction. The initial coordinates (with solvents and ions) for each sampling window were extracted from previous trajectories. The reaction coordinate (bond length difference) of each initial frame was closed to the center of the window. So, need I do energy-minimization and equilibration for each window? Since each initial conformation has no bad clashes (actually they can run MD well without minimizations) and is closed to the window center, I cannot understand why minimization and equilibration are still needed (as a lot of references do so).

I don't think minimization is essential, but unless you saved the full 
state (including velocities) for each snapshot, then you need to 
re-equilibrate. Otherwise you're either starting from T=0 K (gen-vel=no) 
or a random state that is not necessarily stable (gen-vel=yes).

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From jalemkul at vt.edu  Mon Jan 13 14:30:24 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Mon, 13 Jan 2020 13:30:24 -0000
Subject: [gmx-users] cannot load the xtc file (without PBC) to VMD
In-Reply-To: <CAKpt5Pe_zAOZiK18s3V_tzGiHZ3mFkK2e7dfD=7SsocgWYk6rw@mail.gmail.com>
References: <CAKpt5Pe_zAOZiK18s3V_tzGiHZ3mFkK2e7dfD=7SsocgWYk6rw@mail.gmail.com>
Message-ID: <17ca7757-2b0d-7b0b-2ff1-50779610806f@vt.edu>



On 1/13/20 5:35 AM, Lalehan Ozalp wrote:
> Dear all, I have a question regarding loading .xtc file (with no periodic
> boundary conditions) to VMD which I generated before. To this end, I had
> used the command:
> trjconv -f md_0_10.xtc -s md_30.tpr -n index.ndx -o noPBC.xtc -pbc mol -ur
> compact -center
> and selected *protein* for centering, and *system* for output.
> However, when I load my corresponding gro file to VMD, and then loading the
> xtc file above, the following error occurs:
>
> ERROR) BaseMolecule: attempt to init atoms while structure building in
> progress!
> ERROR) Invalid number of atoms in file: 132259
> Info) Using plugin xtc for coordinates from file
> /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc
> ERROR) Incorrect number of atoms (132259) in
> ERROR) coordinate file /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc
> ERROR) Mismatch between existing molecule or structure file atom count and
> coordinate or trajectory file atom count.
> Info) Finished with coordinate file
> /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc.

The error implies you've loaded a mismatched coordinate file for this 
trajectory, or otherwise didn't save the number of coordinates you 
thought you did with trjconv. This is really more of a VMD problem, so 
you may find better support on their mailing list.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From jalemkul at vt.edu  Mon Jan 13 14:31:07 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Mon, 13 Jan 2020 13:31:07 -0000
Subject: [gmx-users] Query regarding do_dssp program
In-Reply-To: <CACgG5G-upuHz8NV9ggCZo08eyzdYXm6n9SYt=daVTw5Y9z2Tug@mail.gmail.com>
References: <CACgG5G_W98HHjQOVfcExjW09-4-93XRCChf5n8Hk6hYsY-XP4g@mail.gmail.com>
	<CANogp5yG74V8SU9o6h4q4NT3P7=vc7r29fXo9PTGym_w5uMS-w@mail.gmail.com>
	<CACgG5G-upuHz8NV9ggCZo08eyzdYXm6n9SYt=daVTw5Y9z2Tug@mail.gmail.com>
Message-ID: <5725d611-97f4-ef09-4ee6-acc151e87884@vt.edu>



On 1/13/20 7:22 AM, Sundari wrote:
> Hello Dear,
>
> Actually I was thinking the same i.e. gromacs use "dssp" criteria and vmd
> use "stride" algorithm for secondary structure determination.
> But the expected error in the two algorithms should not be more than 5%
> according to the literature. Here, In my case, the structure contains a lot
> of beta-sheets by dssp and that sequence in vmd is showing 5-helix instead
> of beta-sheets. I am in a confusion now because I want the snapshots of the
> structures obtained by gromacs dssp.

Are you sure you're looking at the same snapshots? Those are wildly 
different structures. I have had VMD show coils for helices and strands 
before, but never any disagreement to this extent.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From sundi6170 at gmail.com  Mon Jan 13 15:15:45 2020
From: sundi6170 at gmail.com (Sundari)
Date: Mon, 13 Jan 2020 14:15:45 -0000
Subject: [gmx-users] Query regarding do_dssp program
In-Reply-To: <5725d611-97f4-ef09-4ee6-acc151e87884@vt.edu>
References: <CACgG5G_W98HHjQOVfcExjW09-4-93XRCChf5n8Hk6hYsY-XP4g@mail.gmail.com>
	<CANogp5yG74V8SU9o6h4q4NT3P7=vc7r29fXo9PTGym_w5uMS-w@mail.gmail.com>
	<CACgG5G-upuHz8NV9ggCZo08eyzdYXm6n9SYt=daVTw5Y9z2Tug@mail.gmail.com>
	<5725d611-97f4-ef09-4ee6-acc151e87884@vt.edu>
Message-ID: <CACgG5G8bsFiXd13gxVyLFbQb9XQg+GkC6nXP9Kbw_uXJrGTiMA@mail.gmail.com>

Yes, Sir,  I  made the gro file for a particular time by using "gmx
trjconv" command ( also checked with -pbc mol, whole, no_jump options )
but every time the 2ndary structure visualization in vmd is different from
dssp sequence of residues in gromacs. Fox example in my protein dssp shows
8 residues making beta-sheets but when I load that particular time frame in
vmd for visualizing the structure,  these 8 residues showing 5-helix
structure.

Please suggest something.

On Mon, Jan 13, 2020 at 7:01 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/13/20 7:22 AM, Sundari wrote:
> > Hello Dear,
> >
> > Actually I was thinking the same i.e. gromacs use "dssp" criteria and vmd
> > use "stride" algorithm for secondary structure determination.
> > But the expected error in the two algorithms should not be more than 5%
> > according to the literature. Here, In my case, the structure contains a
> lot
> > of beta-sheets by dssp and that sequence in vmd is showing 5-helix
> instead
> > of beta-sheets. I am in a confusion now because I want the snapshots of
> the
> > structures obtained by gromacs dssp.
>
> Are you sure you're looking at the same snapshots? Those are wildly
> different structures. I have had VMD show coils for helices and strands
> before, but never any disagreement to this extent.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From lvqingjiejie at 163.com  Mon Jan 13 15:23:02 2020
From: lvqingjiejie at 163.com (Qing Lv)
Date: Mon, 13 Jan 2020 14:23:02 -0000
Subject: [gmx-users] Is minimization and equilibration needed for
 umbrella sampling?
In-Reply-To: <79319b78-b288-e65b-151c-0269521d7b50@vt.edu>
References: <mailman.497.1578533652.1966.gromacs.org_gmx-users@maillist.sys.kth.se>
	<CABgRApv-9wrniSu1H0jj_Nii0Lb5GK9XiDhaqKMvTNukPP0YKw@mail.gmail.com>
	<4a04883d.c54a.16f90318a6a.Coremail.lvqingjiejie@163.com>
	<79319b78-b288-e65b-151c-0269521d7b50@vt.edu>
Message-ID: <3dde0395.adea.16f9f490c6d.Coremail.lvqingjiejie@163.com>

Thank you, Justin. I start each run by randomly generate velocities at 300K, and each run is quite stable. So, is it appropriate to regard the first 20 ps (this is a QM/MM MD) of each run as the equilibration and just discard this 20 ps in the final wham analysis?


Best,
Qing



At 2020-01-13 21:29:23, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
>On 1/10/20 11:02 AM, Qing Lv wrote:
>> Dear Colleagues,
>>
>>
>> I am doing a QM/MM umbrella sampling to calculate the PMF of an enzymatic reaction. The initial coordinates (with solvents and ions) for each sampling window were extracted from previous trajectories. The reaction coordinate (bond length difference) of each initial frame was closed to the center of the window. So, need I do energy-minimization and equilibration for each window? Since each initial conformation has no bad clashes (actually they can run MD well without minimizations) and is closed to the window center, I cannot understand why minimization and equilibration are still needed (as a lot of references do so).
>
>I don't think minimization is essential, but unless you saved the full 
>state (including velocities) for each snapshot, then you need to 
>re-equilibrate. Otherwise you're either starting from T=0 K (gen-vel=no) 
>or a random state that is not necessarily stable (gen-vel=yes).
>
>-Justin
>
>-- 
>==================================================
>
>Justin A. Lemkul, Ph.D.
>Assistant Professor
>Office: 301 Fralin Hall
>Lab: 303 Engel Hall
>
>Virginia Tech Department of Biochemistry
>340 West Campus Dr.
>Blacksburg, VA 24061
>
>jalemkul at vt.edu | (540) 231-3129
>http://www.thelemkullab.com
>
>==================================================
>
>-- 
>Gromacs Users mailing list
>
>* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
>* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>* For (un)subscribe requests visit
>https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

From deligkaris at gmail.com  Mon Jan 13 15:33:02 2020
From: deligkaris at gmail.com (Christos Deligkaris)
Date: Mon, 13 Jan 2020 14:33:02 -0000
Subject: [gmx-users] atom moved too far
In-Reply-To: <c845c547-8063-edc6-8e9e-6759be70e35f@vt.edu>
References: <CAAHQ3wnYn0XapewAPd0RoAsC0HZLVJ_CjYU5bZOtDPd=u8aw4g@mail.gmail.com>
	<eb6b4386-8d1c-0a69-d59b-bde928a48d87@vt.edu>
	<CAAHQ3wmpoDWc1BNT90XsEARLe9gV=AVCCejonzouFvOtXqefeA@mail.gmail.com>
	<edcb7673-b113-dcc4-810d-125ef89842f5@vt.edu>
	<CAAHQ3wmURZ_x2RCP-pcasra94BOpAZQNtR86xcCSxF88pVjYKQ@mail.gmail.com>
	<c845c547-8063-edc6-8e9e-6759be70e35f@vt.edu>
Message-ID: <CAAHQ3wmva7vF0_gL99=Sk8LiAN96MNLHtR7+eV1HPZBbXyZ=1A@mail.gmail.com>

Justin thank you.

I installed gromacs 2020, just gmx, (not gmx_mpi) and the simulation
is currently at ~75 ns so I think that solved the problem.

It seems to me that I either did something wrong installing gmx_mpi
(gromacs 2018) or I should not run gmx_mpi on a single node.

gmx 2020 also gives ~25% speed up compared to gmx_mpi 2018 (on 12
cores, single node).

Best wishes,

Christos Deligkaris, PhD

On Mon, Jan 6, 2020 at 8:30 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> On 1/6/20 2:59 PM, Christos Deligkaris wrote:
> > Justin, thank you.
> >
> > I have implemented the pull code but that also exhibits the same error when
> > I use 12 cores (failed at about 2ns) and the simulation goes on fine when I
> > use 6 cores (now at about 32 ns).
> >
> > I tried using the v-rescale thermostat (instead of Nose-Hoover) and
> > Parinello-Rahman barostat, which failed. I also tried the v-rescale
> > thermostat and the Berendsen barostat but that also failed. It seems to me
> > that this is not an equilibration issue.
> >
> > So, to summarize, only if I decrease the time step to 0.001 ps or decrease
> > the number of cores seem to allow the calculation to proceed.
> >
> > In this email list, I read that someone else was trying to use different
> > arguments supplied to mdrun (-nt, -ntomp etc) to solve the same problem. Is
> > it possible that the problem arises due to my running gmx_mpi on a single
> > node? This is the command I use in my submission script:
> >
> > mpirun --mca btl tcp,sm,self /opt/gromacs-2018.1/bin/gmx_mpi mdrun -ntomp
> > \$ntomp -v -deffnm "${inputfile%.tpr}"
> >
> > If you think that this is not due to a physics issue I can continue doing
> > calculations with 6 cores and try to install gromacs 2020 (both gmx and
> > gmx_mpi) to see if my problem persists there or not...
>
> If you're running on a single node, there's no need for an external MPI
> library. Perhaps you've got a buggy implementation? Have you tried using
> 12 cores via the built-in thread MPI library?
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

From lvqingjiejie at 163.com  Mon Jan 13 15:33:18 2020
From: lvqingjiejie at 163.com (Qing Lv)
Date: Mon, 13 Jan 2020 14:33:18 -0000
Subject: [gmx-users] Error bar for umbrella sampling?
In-Reply-To: <79319b78-b288-e65b-151c-0269521d7b50@vt.edu>
References: <mailman.497.1578533652.1966.gromacs.org_gmx-users@maillist.sys.kth.se>
	<CABgRApv-9wrniSu1H0jj_Nii0Lb5GK9XiDhaqKMvTNukPP0YKw@mail.gmail.com>
	<4a04883d.c54a.16f90318a6a.Coremail.lvqingjiejie@163.com>
	<79319b78-b288-e65b-151c-0269521d7b50@vt.edu>
Message-ID: <54157628.aeca.16f9f528def.Coremail.lvqingjiejie@163.com>

Dear All,


I wonder if the error bars are necessary for umbrella sampling in PMF calculation? If yes, how should the error bars be calculated? Need I do 2~3 repeats (with different random initial velocites assigned)?


Thanks,
Qing

From deligkaris at gmail.com  Mon Jan 13 15:36:22 2020
From: deligkaris at gmail.com (Christos Deligkaris)
Date: Mon, 13 Jan 2020 14:36:22 -0000
Subject: [gmx-users] com motion and position restraints may cause artifacts
Message-ID: <CAAHQ3wkvyk9UmO_5=YYEVQLhtetEEVwqVXp-jyEY55DgW-sRqg@mail.gmail.com>

dear all,

I installed gromacs 2020 and I now get the following message during
equilibration:

NOTE 1 [file nvt.mdp]:

  Removing center of mass motion in the presence of position
restraints  might cause artifacts

I do not recall seeing this with gromacs 2018. In which cases are
artifacts created? Is it now recommended to not remove the center of
mass motion during equilibration?

Best wishes,

Christos Deligkaris, PhD

From spss4 at iacs.res.in  Mon Jan 13 15:40:23 2020
From: spss4 at iacs.res.in (spss4 at iacs.res.in)
Date: Mon, 13 Jan 2020 14:40:23 -0000
Subject: [gmx-users] cannot load the xtc file (without PBC) to VMD
In-Reply-To: <CAKpt5Pe_zAOZiK18s3V_tzGiHZ3mFkK2e7dfD=7SsocgWYk6rw@mail.gmail.com>
Message-ID: <20200113201632.Horde.ujWF-BePEwYbkgA1VPqH-k7@mailweb.iacs.res.in>

  Hii
Have you tried with the .trr file? Try the same procedure with .trr file.
Thanks
----- Message from Lalehan Ozalp <lalehan.ozalp at gmail.com> ---------
? ? Date: Mon, 13 Jan 2020 13:35:01 +0300
? ? From: Lalehan Ozalp <lalehan.ozalp at gmail.com>
Reply-To: gmx-users at gromacs.org
Subject: [gmx-users] cannot load the xtc file (without PBC) to VMD
? ? ? To: gmx-users at gromacs.org

> Dear all, I have a question regarding loading .xtc file (with no periodic
> boundary conditions) to VMD which I generated before. To this end, I had
> used the command:
> trjconv -f md_0_10.xtc -s md_30.tpr -n index.ndx -o noPBC.xtc -pbc mol -ur
> compact -center
> and selected *protein* for centering, and *system* for output.
> However, when I load my corresponding gro file to VMD, and then loading the
> xtc file above, the following error occurs:
>
> ERROR) BaseMolecule: attempt to init atoms while structure building in
> progress!
> ERROR) Invalid number of atoms in file: 132259
> Info) Using plugin xtc for coordinates from file
> /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc
> ERROR) Incorrect number of atoms (132259) in
> ERROR) coordinate file /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc
> ERROR) Mismatch between existing molecule or structure file atom count and
> coordinate or trajectory file atom count.
> Info) Finished with coordinate file
> /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc.
>
> This is especially strange since I carried out the same procedure several
> times before. Additionally, I have a parallel system (with an isoenzyme of
> the enzyme used here, with the same cofactor and the same ligand) and the
> same steps worked perfectly. As a side note, this happens when I load xtc
> file without PBC, while does not happen when I load xtc file in the
> presence of PBC.
>
> Thank you so much in advance!
> Lalehan
> --
> Gromacs Users mailing list
>
> * Please search the archive at  
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before  
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests  
> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or  
> send a mail to gmx-users-request at gromacs.org.

----- End message from Lalehan Ozalp <lalehan.ozalp at gmail.com> -----

From a.mecklenfeld at tu-braunschweig.de  Mon Jan 13 17:39:04 2020
From: a.mecklenfeld at tu-braunschweig.de (Andreas Mecklenfeld)
Date: Mon, 13 Jan 2020 16:39:04 -0000
Subject: [gmx-users] Number of bins for wham and umbrella sampling / PMF
Message-ID: <87cffc19-c177-a9f9-50c5-97a89c36899f@tu-braunschweig.de>

Dear Gromacs users,

I want to perform umbrella sampling in order to calculate the PMF for 
pulling a molecule from a surface. For evaluation, I use gmx wham with 
bootstrapping, and Gromacs version is 2018.4.
I've noticed that my results strongly depend on the number of bins, with 
peak heights differ in the magnitude of several kJ/mol. The histograms 
display reasonable overlap. I've tried to alter the number of bins to 
search for convergence (starting from default 200, I used up to 10000 
bins), though convergence was not achieved. Is this an expected 
behaviour and is the default 200 a suitable number of bins?

Thanks,
Andreas


-- 
M. Sc. Andreas Mecklenfeld
Technische Universit?t Braunschweig
Institut f?r Thermodynamik
Hans-Sommer-Stra?e 5
38106 Braunschweig
Deutschland / Germany

Tel: +49 (0)531 391-2634
      +49 (0)531 391-65685
Fax: +49 (0)531 391-7814

http://www.ift-bs.de


From vuqv.phys at gmail.com  Mon Jan 13 17:51:47 2020
From: vuqv.phys at gmail.com (Quyen V. Vu)
Date: Mon, 13 Jan 2020 16:51:47 -0000
Subject: [gmx-users] Error bar for umbrella sampling?
In-Reply-To: <54157628.aeca.16f9f528def.Coremail.lvqingjiejie@163.com>
References: <mailman.497.1578533652.1966.gromacs.org_gmx-users@maillist.sys.kth.se>
	<CABgRApv-9wrniSu1H0jj_Nii0Lb5GK9XiDhaqKMvTNukPP0YKw@mail.gmail.com>
	<4a04883d.c54a.16f90318a6a.Coremail.lvqingjiejie@163.com>
	<79319b78-b288-e65b-151c-0269521d7b50@vt.edu>
	<54157628.aeca.16f9f528def.Coremail.lvqingjiejie@163.com>
Message-ID: <CA+CKAfyue=wk7qLevT=V6PgYZ+Rg2sAGc56g_6UgGmWVps_OJg@mail.gmail.com>

Hi there,
The statistical errors can be estimated by g_wham.
Check this article: Hub, J. S., De Groot, B. L., & Van Der Spoel, D.
(2010). G-whams-a free Weighted Histogram Analysis implementation including
robust error and autocorrelation estimates. *Journal of Chemical Theory and
Computation*, *6*(12), 3713?3720. https://doi.org/10.1021/ct100494z



On Mon, Jan 13, 2020 at 3:35 PM Qing Lv <lvqingjiejie at 163.com> wrote:

> Dear All,
>
>
> I wonder if the error bars are necessary for umbrella sampling in PMF
> calculation? If yes, how should the error bars be calculated? Need I do 2~3
> repeats (with different random initial velocites assigned)?
>
>
> Thanks,
> Qing
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alashkov83 at gmail.com  Mon Jan 13 18:02:08 2020
From: alashkov83 at gmail.com (=?UTF-8?B?0JDQu9C10LrRgdCw0L3QtNGAINCb0LDRiNC60L7Qsg==?=)
Date: Mon, 13 Jan 2020 17:02:08 -0000
Subject: [gmx-users] Error bar for umbrella sampling?
In-Reply-To: <54157628.aeca.16f9f528def.Coremail.lvqingjiejie@163.com>
References: <mailman.497.1578533652.1966.gromacs.org_gmx-users@maillist.sys.kth.se>
	<CABgRApv-9wrniSu1H0jj_Nii0Lb5GK9XiDhaqKMvTNukPP0YKw@mail.gmail.com>
	<4a04883d.c54a.16f90318a6a.Coremail.lvqingjiejie@163.com>
	<79319b78-b288-e65b-151c-0269521d7b50@vt.edu>
	<54157628.aeca.16f9f528def.Coremail.lvqingjiejie@163.com>
Message-ID: <CACc8-jwsCaMhepvTAXyw0wh9-JE_O=JaMZdbOmdz4OFJcJ+CWg@mail.gmail.com>

In pymbar package error estimate directly. Example usage this package for
umbrella sampling can be  found on github page for this package
Alexander

??, 13 ???. 2020 ?., 17:35 Qing Lv <lvqingjiejie at 163.com>:

> Dear All,
>
>
> I wonder if the error bars are necessary for umbrella sampling in PMF
> calculation? If yes, how should the error bars be calculated? Need I do 2~3
> repeats (with different random initial velocites assigned)?
>
>
> Thanks,
> Qing
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From lvqingjiejie at 163.com  Tue Jan 14 03:42:46 2020
From: lvqingjiejie at 163.com (Qing Lv)
Date: Tue, 14 Jan 2020 02:42:46 -0000
Subject: [gmx-users] Error bar for umbrella sampling?
In-Reply-To: <CACc8-jwsCaMhepvTAXyw0wh9-JE_O=JaMZdbOmdz4OFJcJ+CWg@mail.gmail.com>
References: <mailman.497.1578533652.1966.gromacs.org_gmx-users@maillist.sys.kth.se>
	<CABgRApv-9wrniSu1H0jj_Nii0Lb5GK9XiDhaqKMvTNukPP0YKw@mail.gmail.com>
	<4a04883d.c54a.16f90318a6a.Coremail.lvqingjiejie@163.com>
	<79319b78-b288-e65b-151c-0269521d7b50@vt.edu>
	<54157628.aeca.16f9f528def.Coremail.lvqingjiejie@163.com>
	<CACc8-jwsCaMhepvTAXyw0wh9-JE_O=JaMZdbOmdz4OFJcJ+CWg@mail.gmail.com>
Message-ID: <c998f4d.332c.16fa1ee7149.Coremail.lvqingjiejie@163.com>

Thank you Alexander and Quyen. I will try these tools.


Qing





At 2020-01-14 01:01:31, "????????? ??????" <alashkov83 at gmail.com> wrote:
>In pymbar package error estimate directly. Example usage this package for
>umbrella sampling can be  found on github page for this package
>Alexander
>
>??, 13 ???. 2020 ?., 17:35 Qing Lv <lvqingjiejie at 163.com>:
>
>> Dear All,
>>
>>
>> I wonder if the error bars are necessary for umbrella sampling in PMF
>> calculation? If yes, how should the error bars be calculated? Need I do 2~3
>> repeats (with different random initial velocites assigned)?
>>
>>
>> Thanks,
>> Qing
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>-- 
>Gromacs Users mailing list
>
>* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
>* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>* For (un)subscribe requests visit
>https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

From miro.astore at gmail.com  Tue Jan 14 03:48:46 2020
From: miro.astore at gmail.com (Miro Astore)
Date: Tue, 14 Jan 2020 02:48:46 -0000
Subject: [gmx-users] Loading topology into vmd
Message-ID: <CAL3MGYSOEEy70Kp+xCeC6vM1FbzN3SV2oDiuyA7ae+TLc7XgxA@mail.gmail.com>

Hello all,

I'm just wondering how people load topologies for systems simulated in
gromacs into vmd. It is very annoying to have bonds that aren't in the
simulation placed in the visualisation. I'm wondering if anyone has a
solution that is easier than simply creating a psf file of the .gro system
as this can be time consuming for systems with strange geometries.

Best, Miro

From shakirashukoor1993 at gmail.com  Tue Jan 14 05:20:14 2020
From: shakirashukoor1993 at gmail.com (shakira shukoor)
Date: Tue, 14 Jan 2020 04:20:14 -0000
Subject: [gmx-users] Error bar for umbrella sampling?
In-Reply-To: <c998f4d.332c.16fa1ee7149.Coremail.lvqingjiejie@163.com>
References: <mailman.497.1578533652.1966.gromacs.org_gmx-users@maillist.sys.kth.se>
	<CABgRApv-9wrniSu1H0jj_Nii0Lb5GK9XiDhaqKMvTNukPP0YKw@mail.gmail.com>
	<4a04883d.c54a.16f90318a6a.Coremail.lvqingjiejie@163.com>
	<79319b78-b288-e65b-151c-0269521d7b50@vt.edu>
	<54157628.aeca.16f9f528def.Coremail.lvqingjiejie@163.com>
	<CACc8-jwsCaMhepvTAXyw0wh9-JE_O=JaMZdbOmdz4OFJcJ+CWg@mail.gmail.com>
	<c998f4d.332c.16fa1ee7149.Coremail.lvqingjiejie@163.com>
Message-ID: <CADV28megFQmiY1Yb8Mspj-oqT998MFXThgU7OBF6MXbwtY4HCw@mail.gmail.com>

Error bar will be directly given from gmx wham by bootstrap method.

On Tue, Jan 14, 2020 at 8:13 AM Qing Lv <lvqingjiejie at 163.com> wrote:

> Thank you Alexander and Quyen. I will try these tools.
>
>
> Qing
>
>
>
>
>
> At 2020-01-14 01:01:31, "????????? ??????" <alashkov83 at gmail.com> wrote:
> >In pymbar package error estimate directly. Example usage this package for
> >umbrella sampling can be  found on github page for this package
> >Alexander
> >
> >??, 13 ???. 2020 ?., 17:35 Qing Lv <lvqingjiejie at 163.com>:
> >
> >> Dear All,
> >>
> >>
> >> I wonder if the error bars are necessary for umbrella sampling in PMF
> >> calculation? If yes, how should the error bars be calculated? Need I do
> 2~3
> >> repeats (with different random initial velocites assigned)?
> >>
> >>
> >> Thanks,
> >> Qing
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >>
> >--
> >Gromacs Users mailing list
> >
> >* Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> >* For (un)subscribe requests visit
> >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.



-- 
*Best Regards*

Shakkira E
PhD student INSPIRE Scholar
Department of Chemistry
sdmdlab.xyz
IIT Patna
Bihta
Patna 801106

From yogesh.rma13 at gmail.com  Tue Jan 14 07:53:41 2020
From: yogesh.rma13 at gmail.com (Yogesh Sharma)
Date: Tue, 14 Jan 2020 06:53:41 -0000
Subject: [gmx-users] charmm gui pdb to gro.
Message-ID: <CACWq+6-SzcA2Y3Ri77UOWa4mATUn7B=cgdcqYK+r7LRzRjy4dg@mail.gmail.com>

Greetings,
hey, I want to convert the charmm gui generated pdb (membrane + protein) to
gromacs readable file.  charmm generated lipids contain hydrogen atoms and
naming differences. I tried doing it manually but couldnt succeed. Is there
any script available for atom renaming and reordering?

I also tried manual packing of POPC molecules from this site (
http://wcm.ucalgary.ca/tieleman/downloads) around oriented protein
extracted from charmm gui bilayer builder but simulation was not successful
probably i couldnot pack it properly (didn't get any error though. packing
was performed using inflategro with shrinking to a final area of 74A^2).
Charmm gui generated output is working fine with water but I want to
perform complete simulation in 54A7 ff due to ligand parameters
availability. hence, i have to convert charmm gui generated output to gro
format. Is there any way around?

From slall at ncbs.res.in  Tue Jan 14 09:42:23 2020
From: slall at ncbs.res.in (Sahil Lall)
Date: Tue, 14 Jan 2020 08:42:23 -0000
Subject: [gmx-users] charmm gui pdb to gro.
In-Reply-To: <CACWq+6-SzcA2Y3Ri77UOWa4mATUn7B=cgdcqYK+r7LRzRjy4dg@mail.gmail.com>
References: <CACWq+6-SzcA2Y3Ri77UOWa4mATUn7B=cgdcqYK+r7LRzRjy4dg@mail.gmail.com>
Message-ID: <330a249ecb1945de4a8d5a0cffedd7ee@ncbs.res.in>

Hey, 

You could use pdb2gmx on the CHARMM-GUI ".pdb" output. The -ignh flag
allows for ignoring preexisting hydrogen atoms if that's really
required. 

Cheers, 

Sahil

On 2020-01-14 12:23, Yogesh Sharma wrote:

> Greetings,
> hey, I want to convert the charmm gui generated pdb (membrane + protein) to
> gromacs readable file.  charmm generated lipids contain hydrogen atoms and
> naming differences. I tried doing it manually but couldnt succeed. Is there
> any script available for atom renaming and reordering?
> 
> I also tried manual packing of POPC molecules from this site (
> http://wcm.ucalgary.ca/tieleman/downloads) around oriented protein
> extracted from charmm gui bilayer builder but simulation was not successful
> probably i couldnot pack it properly (didn't get any error though. packing
> was performed using inflategro with shrinking to a final area of 74A^2).
> Charmm gui generated output is working fine with water but I want to
> perform complete simulation in 54A7 ff due to ligand parameters
> availability. hence, i have to convert charmm gui generated output to gro
> format. Is there any way around?

From lalehan.ozalp at gmail.com  Tue Jan 14 10:54:06 2020
From: lalehan.ozalp at gmail.com (Lalehan Ozalp)
Date: Tue, 14 Jan 2020 09:54:06 -0000
Subject: [gmx-users] cannot load the xtc file (without PBC) to VMD
In-Reply-To: <20200113201632.Horde.ujWF-BePEwYbkgA1VPqH-k7@mailweb.iacs.res.in>
References: <CAKpt5Pe_zAOZiK18s3V_tzGiHZ3mFkK2e7dfD=7SsocgWYk6rw@mail.gmail.com>
	<20200113201632.Horde.ujWF-BePEwYbkgA1VPqH-k7@mailweb.iacs.res.in>
Message-ID: <CAKpt5Pfma8i1+Q2D1Fye7sC8QeQfv+5QiDZUfS458_+XuKf2nA@mail.gmail.com>

Thank you, but I haven't tried with a trr file and actually the last .trr
file I've produced is em.trr.
Thanks,

On Mon, Jan 13, 2020 at 5:40 PM <spss4 at iacs.res.in> wrote:

>   Hii
> Have you tried with the .trr file? Try the same procedure with .trr file.
> Thanks
> ----- Message from Lalehan Ozalp <lalehan.ozalp at gmail.com> ---------
>     Date: Mon, 13 Jan 2020 13:35:01 +0300
>     From: Lalehan Ozalp <lalehan.ozalp at gmail.com>
> Reply-To: gmx-users at gromacs.org
> Subject: [gmx-users] cannot load the xtc file (without PBC) to VMD
>       To: gmx-users at gromacs.org
>
> > Dear all, I have a question regarding loading .xtc file (with no periodic
> > boundary conditions) to VMD which I generated before. To this end, I had
> > used the command:
> > trjconv -f md_0_10.xtc -s md_30.tpr -n index.ndx -o noPBC.xtc -pbc mol
> -ur
> > compact -center
> > and selected *protein* for centering, and *system* for output.
> > However, when I load my corresponding gro file to VMD, and then loading
> the
> > xtc file above, the following error occurs:
> >
> > ERROR) BaseMolecule: attempt to init atoms while structure building in
> > progress!
> > ERROR) Invalid number of atoms in file: 132259
> > Info) Using plugin xtc for coordinates from file
> > /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc
> > ERROR) Incorrect number of atoms (132259) in
> > ERROR) coordinate file
> /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc
> > ERROR) Mismatch between existing molecule or structure file atom count
> and
> > coordinate or trajectory file atom count.
> > Info) Finished with coordinate file
> > /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc.
> >
> > This is especially strange since I carried out the same procedure several
> > times before. Additionally, I have a parallel system (with an isoenzyme
> of
> > the enzyme used here, with the same cofactor and the same ligand) and the
> > same steps worked perfectly. As a side note, this happens when I load xtc
> > file without PBC, while does not happen when I load xtc file in the
> > presence of PBC.
> >
> > Thank you so much in advance!
> > Lalehan
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests
> > visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > send a mail to gmx-users-request at gromacs.org.
>
> ----- End message from Lalehan Ozalp <lalehan.ozalp at gmail.com> -----
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

From spss4 at iacs.res.in  Tue Jan 14 12:51:16 2020
From: spss4 at iacs.res.in (spss4 at iacs.res.in)
Date: Tue, 14 Jan 2020 11:51:16 -0000
Subject: [gmx-users] cannot load the xtc file (without PBC) to VMD
In-Reply-To: <CAKpt5Pfma8i1+Q2D1Fye7sC8QeQfv+5QiDZUfS458_+XuKf2nA@mail.gmail.com>
References: <CAKpt5Pe_zAOZiK18s3V_tzGiHZ3mFkK2e7dfD=7SsocgWYk6rw@mail.gmail.com>
	<20200113201632.Horde.ujWF-BePEwYbkgA1VPqH-k7@mailweb.iacs.res.in>
	<CAKpt5Pfma8i1+Q2D1Fye7sC8QeQfv+5QiDZUfS458_+XuKf2nA@mail.gmail.com>
Message-ID: <20200114172730.Horde.XOFN7xBMtbeJ6JWeagMqDAk@mailweb.iacs.res.in>

  I didn't get you. So your problem is solved using trr file or not?
----- Message from Lalehan Ozalp <lalehan.ozalp at gmail.com> ---------
? ? Date: Tue, 14 Jan 2020 12:53:54 +0300
? ? From: Lalehan Ozalp <lalehan.ozalp at gmail.com>
Reply-To: gmx-users at gromacs.org
Subject: Re: [gmx-users] cannot load the xtc file (without PBC) to VMD
? ? ? To: gmx-users at gromacs.org

> Thank you, but I haven't tried with a trr file and actually the last .trr
> file I've produced is em.trr.
> Thanks,
>
> On Mon, Jan 13, 2020 at 5:40 PM <spss4 at iacs.res.in> wrote:
>
>> Hii
>> Have you tried with the .trr file? Try the same procedure with .trr file.
>> Thanks
>> ----- Message from Lalehan Ozalp <lalehan.ozalp at gmail.com> ---------
>> ? ? Date: Mon, 13 Jan 2020 13:35:01 +0300
>> ? ? From: Lalehan Ozalp <lalehan.ozalp at gmail.com>
>> Reply-To: gmx-users at gromacs.org
>> Subject: [gmx-users] cannot load the xtc file (without PBC) to VMD
>> ? ? ? To: gmx-users at gromacs.org
>>
>> Dear all, I have a question regarding loading .xtc file (with no periodic
>> boundary conditions) to VMD which I generated before. To this end, I had
>> used the command:
>> trjconv -f md_0_10.xtc -s md_30.tpr -n index.ndx -o noPBC.xtc -pbc mol
>> -ur
>> compact -center
>> and selected *protein* for centering, and *system* for output.
>> However, when I load my corresponding gro file to VMD, and then loading
>> the
>> xtc file above, the following error occurs:
>>
>> ERROR) BaseMolecule: attempt to init atoms while structure building in
>> progress!
>> ERROR) Invalid number of atoms in file: 132259
>> Info) Using plugin xtc for coordinates from file
>> /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc
>> ERROR) Incorrect number of atoms (132259) in
>> ERROR) coordinate file
>> /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc
>> ERROR) Mismatch between existing molecule or structure file atom count
>> and
>> coordinate or trajectory file atom count.
>> Info) Finished with coordinate file
>> /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc.
>>
>> This is especially strange since I carried out the same procedure several
>> times before. Additionally, I have a parallel system (with an isoenzyme
>> of
>> the enzyme used here, with the same cofactor and the same ligand) and the
>> same steps worked perfectly. As a side note, this happens when I load xtc
>> file without PBC, while does not happen when I load xtc file in the
>> presence of PBC.
>>
>> Thank you so much in advance!
>> Lalehan
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests
>> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>> or
>> send a mail to gmx-users-request at gromacs.org.
>>
>> ----- End message from Lalehan Ozalp <lalehan.ozalp at gmail.com> -----
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at  
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before  
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests  
> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or  
> send a mail to gmx-users-request at gromacs.org.

----- End message from Lalehan Ozalp <lalehan.ozalp at gmail.com> -----

From yogesh.rma13 at gmail.com  Tue Jan 14 14:49:21 2020
From: yogesh.rma13 at gmail.com (Yogesh Sharma)
Date: Tue, 14 Jan 2020 13:49:21 -0000
Subject: [gmx-users] charmm gui pdb to gro
Message-ID: <CACWq+6-S8kR6Tbd0ABbcrd+9_TzJxrOrYd1mgoz-=LmPGq73AQ@mail.gmail.com>

*thanks sahil *
*but i am interested in lipid molecule conversion not protein. I think
pdb2gmx will work for protein molecules only.*

From ahernandez at unistra.fr  Tue Jan 14 15:04:40 2020
From: ahernandez at unistra.fr (HERNANDEZ ALBA Oscar (IPHC))
Date: Tue, 14 Jan 2020 14:04:40 -0000
Subject: [gmx-users] inter-chain disulfide bridges
Message-ID: <005f01d5cae2$beec3b30$3cc4b190$@unistra.fr>

Hello everyone,



     I have a problem related with a molecule with inter- and intra-chain
disulfide bridges. When I convert my pdb file into a gromacs file, all the
disulfide bridges are still connected (inter- and intra-chain). However,
when I perform a short optimization of the structure (in vacuum), the
inter-chain disulfide bridges are broken because the bond distance is too
large (around 5 and 6 ?). My idea is to use distance restraint to ?limit?
the maximum distance between the different sulfure atoms to roughly 2 ?.
However, my problem is that I do not know what residue names I have to use
to differentiate the sulfuret atoms from different chains. Below, you can
find two cysteines (from the itp file) from different chains that I would
like to bind. The question is: If I want to use distance restraint between
these two residues, what is the information that I have to put in the ai
and aj fields of the position restraint table?



     Thank you very much for your help and happy new year for all of you.



     Oscar



                                               CYS in chain A

; residue 897 CYS rtp CYS2 q  0.0

   315        NH1    897    CYS      N    315      -0.47     14.007   ;
qtot 2.53

   316          H    897    CYS     HN    316       0.31      1.008   ;
qtot 2.84

   317        CT1    897    CYS     CA    317       0.07     12.011   ;
qtot 2.91

   318         HB    897    CYS     HA    318       0.09      1.008   ;
qtot 3

   319        CT2    897    CYS     CB    319       -0.1     12.011   ;
qtot 2.9

   320         HA    897    CYS    HB1    320       0.09      1.008   ;
qtot 2.99

   321         HA    897    CYS    HB2    321       0.09      1.008   ;
qtot 3.08

   322         SM    897    CYS     SG    322      -0.08      32.06   ;
qtot 3

   323          C    897    CYS      C    323       0.51     12.011   ;
qtot 3.51

   324          O    897    CYS      O    324      -0.51     15.999   ;
qtot 3



                                               CYS in chain B

; residue 445 CYS rtp CYS  q  0.0

  3451        NH1    445    CYS      N   3451      -0.47     14.007   ;
qtot 5.53

  3452          H    445    CYS     HN   3452       0.31      1.008   ;
qtot 5.84

  3453        CT1    445    CYS     CA   3453       0.07     12.011   ;
qtot 5.91

  3454         HB    445    CYS     HA   3454       0.09      1.008   ;
qtot 6

  3455        CT2    445    CYS     CB   3455      -0.11     12.011   ;
qtot 5.89

  3456         HA    445    CYS    HB1   3456       0.09      1.008   ;
qtot 5.98

  3457         HA    445    CYS    HB2   3457       0.09      1.008   ;
qtot 6.07

  3458          S    445    CYS     SG   3458      -0.23      32.06   ;
qtot 5.84

  3459         HS    445    CYS    HG1   3459       0.16      1.008   ;
qtot 6

  3460          C    445    CYS      C   3460       0.51     12.011   ;
qtot 6.51

  3461          O    445    CYS      O   3461      -0.51     15.999   ;
qtot 6




From goossens_kenny at hotmail.com  Tue Jan 14 16:19:42 2020
From: goossens_kenny at hotmail.com (Kenny Goossens)
Date: Tue, 14 Jan 2020 15:19:42 -0000
Subject: [gmx-users] Loading topology into vmd
In-Reply-To: <CAL3MGYSOEEy70Kp+xCeC6vM1FbzN3SV2oDiuyA7ae+TLc7XgxA@mail.gmail.com>
References: <CAL3MGYSOEEy70Kp+xCeC6vM1FbzN3SV2oDiuyA7ae+TLc7XgxA@mail.gmail.com>
Message-ID: <AM0PR01MB65149E6F31C527A89BAFA946F8340@AM0PR01MB6514.eurprd01.prod.exchangelabs.com>

Hi,

I'm not sure what you mean by "bonds that aren't in the simulation", but from my experience, converting your .gro file with gmx trjconv using the -pbc mol and -ur compact options usually gives a clean visualisation. If necessary, you can also use the -center option to center a specific structure/residue in the box. You can have the output written in the .gro file format, or convert to anything more convenient.

With kind regards,
______________________________
Kenneth Goossens, PhD student
Laboratory of Medicinal Chemistry (Building A - Room 2.13)
University of Antwerp - Campus Drie Eiken
Universiteitsplein 1
B-2610 Wilrijk
Belgium



________________________________
Van: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> namens Miro Astore <miro.astore at gmail.com>
Verzonden: dinsdag 14 januari 2020 3:48
Aan: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
Onderwerp: [gmx-users] Loading topology into vmd

Hello all,

I'm just wondering how people load topologies for systems simulated in
gromacs into vmd. It is very annoying to have bonds that aren't in the
simulation placed in the visualisation. I'm wondering if anyone has a
solution that is easier than simply creating a psf file of the .gro system
as this can be time consuming for systems with strange geometries.

Best, Miro
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

From travis.meyer at rutgers.edu  Tue Jan 14 19:40:55 2020
From: travis.meyer at rutgers.edu (Travis Meyer)
Date: Tue, 14 Jan 2020 18:40:55 -0000
Subject: [gmx-users] Troubleshooting Error Message: Invalid Index Group
	References
Message-ID: <BN8PR14MB317166F8297AB07F3187B89693340@BN8PR14MB3171.namprd14.prod.outlook.com>

Hello all,

I am a brand new MD/GROMACS user, and I have been trying to learn how to use GROMACS for coarse-grained simulations using the MARTINI forcefield. I was going through a tutorial on coarse-graining from the MARTINI website (http://cgmartini.nl/index.php/tutorials-general-introduction-gmx5/martini-tutorials-polymers-gmx5) but ran into an error I have been not been able to find a solution for.

After coarse-graining the all-atom simulation to the COM between 3 atoms, I need to calculate bond lengths and angles in order to parameterize bonded interactions. Following instructions from the tutorial, I created index files for all bonds, angles, and dihedrals and used gmx distance along with the coarse-grained trajectory file. After choosing which index group I want to use, I receive an error message:

Inconsistency in user input: Invalid index group references encountered
Group 'bonds_core1' cannot be used in selections, because it contains negative atom indices and/or references atoms not present (largest allowed atom index is 0).

The index file itself contains all the proper atom indices. The fact that the error says "largest allowed atom index is 0" makes me think there is an error with my .xtc file, but I did not receive any errors when calculating angle distributions using the exact same trajectory file and appropriate angle index files.

Are there any recommendations for how to go about fixing this?

Thanks!

From dmaji43 at gmail.com  Tue Jan 14 20:28:51 2020
From: dmaji43 at gmail.com (Dhrubajyoti Maji)
Date: Tue, 14 Jan 2020 19:28:51 -0000
Subject: [gmx-users] cut-off scheme
Message-ID: <CACrPy4B7niyieTA7X_vPVap5VdMS5Ed1p5JRvr47spb=ZmOFmA@mail.gmail.com>

Dear all,
         I have found in some old literatures where force field
parmetrizations were done, they have used group cut-off scheme which was
default in gromacs version then. Now, if I want to use those parameters in
updated gromacs version, do I have to take cutoff scheme as group ? Or can
I use Verlet as it is default now? Any kind of help will be appreciated.
Thanks and regards,
Dhrubajyoti Maji

From miro.astore at gmail.com  Tue Jan 14 20:57:32 2020
From: miro.astore at gmail.com (Miro Astore)
Date: Tue, 14 Jan 2020 19:57:32 -0000
Subject: [gmx-users] Loading topology into vmd
In-Reply-To: <AM0PR01MB65149E6F31C527A89BAFA946F8340@AM0PR01MB6514.eurprd01.prod.exchangelabs.com>
References: <CAL3MGYSOEEy70Kp+xCeC6vM1FbzN3SV2oDiuyA7ae+TLc7XgxA@mail.gmail.com>
	<AM0PR01MB65149E6F31C527A89BAFA946F8340@AM0PR01MB6514.eurprd01.prod.exchangelabs.com>
Message-ID: <CAL3MGYQ1X0EndBb8o1_pVpcBKW6J3QiYEYhEUueB7TtjVYq=nQ@mail.gmail.com>

Hi kenny, thanks for getting back to me.

I use something similar to what you've suggested to deal with periodic
boundary conditions. My current issue is that vmd will place a bond between
two atoms that are close together in the first frame of the visualization
even if those atoms aren't linked in the topology. The fake bonds are then
kept throughout the visualization . That is, when I load just a gro and a
trr.

A psf file would fix this situation but my efforts to recreate a whole one
from my complex system using top2psf.pl hasn't borne much fruit.

Just wondering what other people have tried.

Best, Miro

Le mer. 15 janv. 2020 ? 02:20, Kenny Goossens <goossens_kenny at hotmail.com>
a ?crit :

> Hi,
>
> I'm not sure what you mean by "bonds that aren't in the simulation", but
> from my experience, converting your .gro file with gmx trjconv using the
> -pbc mol and -ur compact options usually gives a clean visualisation. If
> necessary, you can also use the -center option to center a specific
> structure/residue in the box. You can have the output written in the .gro
> file format, or convert to anything more convenient.
>
> With kind regards,
> ______________________________
> Kenneth Goossens, PhD student
> Laboratory of Medicinal Chemistry (Building A - Room 2.13)
> University of Antwerp - Campus Drie Eiken
> Universiteitsplein 1
> B-2610 Wilrijk
> Belgium
>
>
>
> ________________________________
> Van: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> namens Miro Astore <
> miro.astore at gmail.com>
> Verzonden: dinsdag 14 januari 2020 3:48
> Aan: gromacs.org_gmx-users at maillist.sys.kth.se <
> gromacs.org_gmx-users at maillist.sys.kth.se>
> Onderwerp: [gmx-users] Loading topology into vmd
>
> Hello all,
>
> I'm just wondering how people load topologies for systems simulated in
> gromacs into vmd. It is very annoying to have bonds that aren't in the
> simulation placed in the visualisation. I'm wondering if anyone has a
> solution that is easier than simply creating a psf file of the .gro system
> as this can be time consuming for systems with strange geometries.
>
> Best, Miro
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From rabetayeasmin at gmail.com  Tue Jan 14 23:35:47 2020
From: rabetayeasmin at gmail.com (Rabeta Yeasmin)
Date: Tue, 14 Jan 2020 22:35:47 -0000
Subject: [gmx-users] Calculating C-alpha RMSD for coarse grained simulation
Message-ID: <CAB5hSou=vDLmW2FWi0dUptyJLO1DH92w2oa2iX2djatHnuA4jg@mail.gmail.com>

Hi,

I am new user of GROMACS. I have run coarse-grained umbrella sampling
simulation in GROMACS. I had prepared the system in CHARMM-GUI. After
running the simulation, now I want to calculate the RMSD of the protein. I
have used the following command to remove pbc effect first-
gmx trjconv -s 0A.gro -f 0A-2.xtc -o 0A-2-pbc.xtc -pbc nojump -ur compact
-n index-all.ndx

And then used the following command to calculate the RMSD-

gmx rms -s step6.0_minimization.tpr -f 0A-2-pbc.xtc -fit rot+trans  -o
rmsd-2 -pbc

But after running the command, it asks to select group of least square fit,
I choose protein and the RMSD value is too high around 3.5 nm. Can you
please help me how I can calculate RMSD for coarse grained protein?

Thanks.

Rabeta Yeasmin

From sadafrani6 at gmail.com  Wed Jan 15 00:33:08 2020
From: sadafrani6 at gmail.com (Sadaf Rani)
Date: Tue, 14 Jan 2020 23:33:08 -0000
Subject: [gmx-users] A list of missing interactions
Message-ID: <CAH9Uu9PfmNEdMs1gx7iQ0Oz6R98z+guMNDqMsHz2VD0k6YpRLw@mail.gmail.com>

Dear Gromacs users
I am facing this error during free energy calculation of protein-ligand for
which I have applied restrained to some atoms of protein residue and
ligand.
A list of missing interactions:
      Restraint Pot. of      1 missing      1

Molecule type 'Protein'
the first 10 missing interactions, except for exclusions:
      Restraint Pot. atoms 3437 7908           global  3437  7908

-------------------------------------------------------
Program:     gmx mdrun, version 2018.1
Source file: src/gromacs/domdec/domdec_topology.cpp (line 436)
MPI rank:    0 (out of 2)

Fatal error:
1 of the 64584 bonded interactions could not be calculated because some
atoms
involved moved further apart than the multi-body cut-off distance (4.47682
nm)
or the two-body cut-off distance (4.47682 nm), see option -rdd, for pairs
and
tabulated bonds also see option -ddcheck

Could anybody please suggest how should I fix this error? I would be really
thankful.

Regards

Sadaf

From jalemkul at vt.edu  Wed Jan 15 03:14:56 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Wed, 15 Jan 2020 02:14:56 -0000
Subject: [gmx-users] Query regarding do_dssp program
In-Reply-To: <CACgG5G8bsFiXd13gxVyLFbQb9XQg+GkC6nXP9Kbw_uXJrGTiMA@mail.gmail.com>
References: <CACgG5G_W98HHjQOVfcExjW09-4-93XRCChf5n8Hk6hYsY-XP4g@mail.gmail.com>
	<CANogp5yG74V8SU9o6h4q4NT3P7=vc7r29fXo9PTGym_w5uMS-w@mail.gmail.com>
	<CACgG5G-upuHz8NV9ggCZo08eyzdYXm6n9SYt=daVTw5Y9z2Tug@mail.gmail.com>
	<5725d611-97f4-ef09-4ee6-acc151e87884@vt.edu>
	<CACgG5G8bsFiXd13gxVyLFbQb9XQg+GkC6nXP9Kbw_uXJrGTiMA@mail.gmail.com>
Message-ID: <a8c319c9-dc32-afec-a96c-9dd2e843039a@vt.edu>



On 1/13/20 9:15 AM, Sundari wrote:
> Yes, Sir,  I  made the gro file for a particular time by using "gmx
> trjconv" command ( also checked with -pbc mol, whole, no_jump options )
> but every time the 2ndary structure visualization in vmd is different from
> dssp sequence of residues in gromacs. Fox example in my protein dssp shows
> 8 residues making beta-sheets but when I load that particular time frame in
> vmd for visualizing the structure,  these 8 residues showing 5-helix
> structure.
>
> Please suggest something.

I'm afraid I can't. Those are two completely different hydrogen bonding 
patterns and I can't imagine how the algorithms would differ so 
dramatically. I have seen VMD render coils for helices and sheets but 
never a totally different secondary structure. Be sure you're telling 
VMD to re-compute structures and re-color the secondary structure 
elements at every snapshot for trajectory visualization, otherwise it 
will render everything the same as the initial frame, which will 
obviously be wrong in the case of large structural changes.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From jalemkul at vt.edu  Wed Jan 15 03:15:23 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Wed, 15 Jan 2020 02:15:23 -0000
Subject: [gmx-users] Is minimization and equilibration needed for
 umbrella sampling?
In-Reply-To: <3dde0395.adea.16f9f490c6d.Coremail.lvqingjiejie@163.com>
References: <mailman.497.1578533652.1966.gromacs.org_gmx-users@maillist.sys.kth.se>
	<CABgRApv-9wrniSu1H0jj_Nii0Lb5GK9XiDhaqKMvTNukPP0YKw@mail.gmail.com>
	<4a04883d.c54a.16f90318a6a.Coremail.lvqingjiejie@163.com>
	<79319b78-b288-e65b-151c-0269521d7b50@vt.edu>
	<3dde0395.adea.16f9f490c6d.Coremail.lvqingjiejie@163.com>
Message-ID: <ccc20fe7-ce78-48d6-2155-fcac92598e42@vt.edu>



On 1/13/20 9:22 AM, Qing Lv wrote:
> Thank you, Justin. I start each run by randomly generate velocities at 300K, and each run is quite stable. So, is it appropriate to regard the first 20 ps (this is a QM/MM MD) of each run as the equilibration and just discard this 20 ps in the final wham analysis?

If 20 ps is sufficient equilibration, sure.

-Justin

>
> Best,
> Qing
>
>
>
> At 2020-01-13 21:29:23, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>>
>> On 1/10/20 11:02 AM, Qing Lv wrote:
>>> Dear Colleagues,
>>>
>>>
>>> I am doing a QM/MM umbrella sampling to calculate the PMF of an enzymatic reaction. The initial coordinates (with solvents and ions) for each sampling window were extracted from previous trajectories. The reaction coordinate (bond length difference) of each initial frame was closed to the center of the window. So, need I do energy-minimization and equilibration for each window? Since each initial conformation has no bad clashes (actually they can run MD well without minimizations) and is closed to the window center, I cannot understand why minimization and equilibration are still needed (as a lot of references do so).
>> I don't think minimization is essential, but unless you saved the full
>> state (including velocities) for each snapshot, then you need to
>> re-equilibrate. Otherwise you're either starting from T=0 K (gen-vel=no)
>> or a random state that is not necessarily stable (gen-vel=yes).
>>
>> -Justin
>>
>> -- 
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
>> -- 
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From bhupendra.dandekar001 at gmail.com  Wed Jan 15 04:57:44 2020
From: bhupendra.dandekar001 at gmail.com (Bhupendra Dandekar)
Date: Wed, 15 Jan 2020 03:57:44 -0000
Subject: [gmx-users] Calculating C-alpha RMSD for coarse grained
	simulation
In-Reply-To: <CAB5hSou=vDLmW2FWi0dUptyJLO1DH92w2oa2iX2djatHnuA4jg@mail.gmail.com>
References: <CAB5hSou=vDLmW2FWi0dUptyJLO1DH92w2oa2iX2djatHnuA4jg@mail.gmail.com>
Message-ID: <CA+jgKGUotOFCVgruEAw9gkddKFRqVQ+RBURW9iuc-Vhaa1vo4A@mail.gmail.com>

Dear Rebeta

Did you visualise your trajectory? If not then kindly first do that.
If the protein in your CG simulation is fluctuating a lot then the rmsd of
3.5 can make sense.

Also, prepare a separate index for protein BB(backbone) bead only and use
it in rmsd fitting as well as rmsd calculation. There might be large
fluctuations in the sidechains compared to protein backbone which is giving
the resulting higher value of rmsd than expected.

Best wishes.
Bhupendra


On Wed, Jan 15, 2020 at 4:06 AM Rabeta Yeasmin <rabetayeasmin at gmail.com>
wrote:

> Hi,
>
> I am new user of GROMACS. I have run coarse-grained umbrella sampling
> simulation in GROMACS. I had prepared the system in CHARMM-GUI. After
> running the simulation, now I want to calculate the RMSD of the protein. I
> have used the following command to remove pbc effect first-
> gmx trjconv -s 0A.gro -f 0A-2.xtc -o 0A-2-pbc.xtc -pbc nojump -ur compact
> -n index-all.ndx
>
> And then used the following command to calculate the RMSD-
>
> gmx rms -s step6.0_minimization.tpr -f 0A-2-pbc.xtc -fit rot+trans  -o
> rmsd-2 -pbc
>
> But after running the command, it asks to select group of least square fit,
> I choose protein and the RMSD value is too high around 3.5 nm. Can you
> please help me how I can calculate RMSD for coarse grained protein?
>
> Thanks.
>
> Rabeta Yeasmin
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From bhupendra.dandekar001 at gmail.com  Wed Jan 15 04:57:44 2020
From: bhupendra.dandekar001 at gmail.com (Bhupendra Dandekar)
Date: Wed, 15 Jan 2020 03:57:44 -0000
Subject: [gmx-users] Calculating C-alpha RMSD for coarse grained
	simulation
In-Reply-To: <CAB5hSou=vDLmW2FWi0dUptyJLO1DH92w2oa2iX2djatHnuA4jg@mail.gmail.com>
References: <CAB5hSou=vDLmW2FWi0dUptyJLO1DH92w2oa2iX2djatHnuA4jg@mail.gmail.com>
Message-ID: <CA+jgKGUotOFCVgruEAw9gkddKFRqVQ+RBURW9iuc-Vhaa1vo4A@mail.gmail.com>

Dear Rebeta

Did you visualise your trajectory? If not then kindly first do that.
If the protein in your CG simulation is fluctuating a lot then the rmsd of
3.5 can make sense.

Also, prepare a separate index for protein BB(backbone) bead only and use
it in rmsd fitting as well as rmsd calculation. There might be large
fluctuations in the sidechains compared to protein backbone which is giving
the resulting higher value of rmsd than expected.

Best wishes.
Bhupendra


On Wed, Jan 15, 2020 at 4:06 AM Rabeta Yeasmin <rabetayeasmin at gmail.com>
wrote:

> Hi,
>
> I am new user of GROMACS. I have run coarse-grained umbrella sampling
> simulation in GROMACS. I had prepared the system in CHARMM-GUI. After
> running the simulation, now I want to calculate the RMSD of the protein. I
> have used the following command to remove pbc effect first-
> gmx trjconv -s 0A.gro -f 0A-2.xtc -o 0A-2-pbc.xtc -pbc nojump -ur compact
> -n index-all.ndx
>
> And then used the following command to calculate the RMSD-
>
> gmx rms -s step6.0_minimization.tpr -f 0A-2-pbc.xtc -fit rot+trans  -o
> rmsd-2 -pbc
>
> But after running the command, it asks to select group of least square fit,
> I choose protein and the RMSD value is too high around 3.5 nm. Can you
> please help me how I can calculate RMSD for coarse grained protein?
>
> Thanks.
>
> Rabeta Yeasmin
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From sundi6170 at gmail.com  Wed Jan 15 06:27:38 2020
From: sundi6170 at gmail.com (Sundari)
Date: Wed, 15 Jan 2020 05:27:38 -0000
Subject: [gmx-users] Query regarding do_dssp program
In-Reply-To: <a8c319c9-dc32-afec-a96c-9dd2e843039a@vt.edu>
References: <CACgG5G_W98HHjQOVfcExjW09-4-93XRCChf5n8Hk6hYsY-XP4g@mail.gmail.com>
	<CANogp5yG74V8SU9o6h4q4NT3P7=vc7r29fXo9PTGym_w5uMS-w@mail.gmail.com>
	<CACgG5G-upuHz8NV9ggCZo08eyzdYXm6n9SYt=daVTw5Y9z2Tug@mail.gmail.com>
	<5725d611-97f4-ef09-4ee6-acc151e87884@vt.edu>
	<CACgG5G8bsFiXd13gxVyLFbQb9XQg+GkC6nXP9Kbw_uXJrGTiMA@mail.gmail.com>
	<a8c319c9-dc32-afec-a96c-9dd2e843039a@vt.edu>
Message-ID: <CACgG5G8SsEKvZJ7SGmDUd61scjv+A6LOrM3RWAs1bjxa2Ewnkw@mail.gmail.com>

I tried all the options.. I load gro file instead of xtc. At zero frame I
gave representations new cartoon + secondary structure.. then I calculate
sec str details by going on vmd timeline.
I don't know what I am missing.. I am doing the same which I used all the
time.
Because these are two totally different secondary structures that's why I
was worrying.. because these are major structures one reports so Very
important to resolve this issue.

On Wednesday, January 15, 2020, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/13/20 9:15 AM, Sundari wrote:
>
>> Yes, Sir,  I  made the gro file for a particular time by using "gmx
>> trjconv" command ( also checked with -pbc mol, whole, no_jump options )
>> but every time the 2ndary structure visualization in vmd is different from
>> dssp sequence of residues in gromacs. Fox example in my protein dssp shows
>> 8 residues making beta-sheets but when I load that particular time frame
>> in
>> vmd for visualizing the structure,  these 8 residues showing 5-helix
>> structure.
>>
>> Please suggest something.
>>
>
> I'm afraid I can't. Those are two completely different hydrogen bonding
> patterns and I can't imagine how the algorithms would differ so
> dramatically. I have seen VMD render coils for helices and sheets but never
> a totally different secondary structure. Be sure you're telling VMD to
> re-compute structures and re-color the secondary structure elements at
> every snapshot for trajectory visualization, otherwise it will render
> everything the same as the initial frame, which will obviously be wrong in
> the case of large structural changes.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Wed Jan 15 09:35:13 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Wed, 15 Jan 2020 08:35:13 -0000
Subject: [gmx-users] Loading topology into vmd
In-Reply-To: <CAL3MGYQ1X0EndBb8o1_pVpcBKW6J3QiYEYhEUueB7TtjVYq=nQ@mail.gmail.com>
References: <CAL3MGYSOEEy70Kp+xCeC6vM1FbzN3SV2oDiuyA7ae+TLc7XgxA@mail.gmail.com>
	<AM0PR01MB65149E6F31C527A89BAFA946F8340@AM0PR01MB6514.eurprd01.prod.exchangelabs.com>
	<CAL3MGYQ1X0EndBb8o1_pVpcBKW6J3QiYEYhEUueB7TtjVYq=nQ@mail.gmail.com>
Message-ID: <CANogp5wFaYi_DFLMU7GiqzZvh+-s9wQbAvf=4NAvmftsyXKQ6A@mail.gmail.com>

Hi,
One of the criteria that VMD uses to define bond is distance criteria. When
you source your gro file, this criteria is applied.
One way one, I have used is to not visualize  undesired bonds, is the
following:
delete the undesired bonds, save the vmd setting (*.vmd file),  load the
setting before any of the following visualizations.
That is not the most elegant way, but it works in my case.
For more elegant ways, you could ask to VMD maillist.
Best regards
Alessandra


On Tue, Jan 14, 2020 at 8:59 PM Miro Astore <miro.astore at gmail.com> wrote:

> Hi kenny, thanks for getting back to me.
>
> I use something similar to what you've suggested to deal with periodic
> boundary conditions. My current issue is that vmd will place a bond between
> two atoms that are close together in the first frame of the visualization
> even if those atoms aren't linked in the topology. The fake bonds are then
> kept throughout the visualization . That is, when I load just a gro and a
> trr.
>
> A psf file would fix this situation but my efforts to recreate a whole one
> from my complex system using top2psf.pl hasn't borne much fruit.
>
> Just wondering what other people have tried.
>
> Best, Miro
>
> Le mer. 15 janv. 2020 ? 02:20, Kenny Goossens <goossens_kenny at hotmail.com>
> a ?crit :
>
> > Hi,
> >
> > I'm not sure what you mean by "bonds that aren't in the simulation", but
> > from my experience, converting your .gro file with gmx trjconv using the
> > -pbc mol and -ur compact options usually gives a clean visualisation. If
> > necessary, you can also use the -center option to center a specific
> > structure/residue in the box. You can have the output written in the .gro
> > file format, or convert to anything more convenient.
> >
> > With kind regards,
> > ______________________________
> > Kenneth Goossens, PhD student
> > Laboratory of Medicinal Chemistry (Building A - Room 2.13)
> > University of Antwerp - Campus Drie Eiken
> > Universiteitsplein 1
> > B-2610 Wilrijk
> > Belgium
> >
> >
> >
> > ________________________________
> > Van: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> namens Miro Astore <
> > miro.astore at gmail.com>
> > Verzonden: dinsdag 14 januari 2020 3:48
> > Aan: gromacs.org_gmx-users at maillist.sys.kth.se <
> > gromacs.org_gmx-users at maillist.sys.kth.se>
> > Onderwerp: [gmx-users] Loading topology into vmd
> >
> > Hello all,
> >
> > I'm just wondering how people load topologies for systems simulated in
> > gromacs into vmd. It is very annoying to have bonds that aren't in the
> > simulation placed in the visualisation. I'm wondering if anyone has a
> > solution that is easier than simply creating a psf file of the .gro
> system
> > as this can be time consuming for systems with strange geometries.
> >
> > Best, Miro
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

From alessandra.villa.biosim at gmail.com  Wed Jan 15 09:35:14 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Wed, 15 Jan 2020 08:35:14 -0000
Subject: [gmx-users] Loading topology into vmd
In-Reply-To: <CAL3MGYQ1X0EndBb8o1_pVpcBKW6J3QiYEYhEUueB7TtjVYq=nQ@mail.gmail.com>
References: <CAL3MGYSOEEy70Kp+xCeC6vM1FbzN3SV2oDiuyA7ae+TLc7XgxA@mail.gmail.com>
	<AM0PR01MB65149E6F31C527A89BAFA946F8340@AM0PR01MB6514.eurprd01.prod.exchangelabs.com>
	<CAL3MGYQ1X0EndBb8o1_pVpcBKW6J3QiYEYhEUueB7TtjVYq=nQ@mail.gmail.com>
Message-ID: <CANogp5wFaYi_DFLMU7GiqzZvh+-s9wQbAvf=4NAvmftsyXKQ6A@mail.gmail.com>

Hi,
One of the criteria that VMD uses to define bond is distance criteria. When
you source your gro file, this criteria is applied.
One way one, I have used is to not visualize  undesired bonds, is the
following:
delete the undesired bonds, save the vmd setting (*.vmd file),  load the
setting before any of the following visualizations.
That is not the most elegant way, but it works in my case.
For more elegant ways, you could ask to VMD maillist.
Best regards
Alessandra


On Tue, Jan 14, 2020 at 8:59 PM Miro Astore <miro.astore at gmail.com> wrote:

> Hi kenny, thanks for getting back to me.
>
> I use something similar to what you've suggested to deal with periodic
> boundary conditions. My current issue is that vmd will place a bond between
> two atoms that are close together in the first frame of the visualization
> even if those atoms aren't linked in the topology. The fake bonds are then
> kept throughout the visualization . That is, when I load just a gro and a
> trr.
>
> A psf file would fix this situation but my efforts to recreate a whole one
> from my complex system using top2psf.pl hasn't borne much fruit.
>
> Just wondering what other people have tried.
>
> Best, Miro
>
> Le mer. 15 janv. 2020 ? 02:20, Kenny Goossens <goossens_kenny at hotmail.com>
> a ?crit :
>
> > Hi,
> >
> > I'm not sure what you mean by "bonds that aren't in the simulation", but
> > from my experience, converting your .gro file with gmx trjconv using the
> > -pbc mol and -ur compact options usually gives a clean visualisation. If
> > necessary, you can also use the -center option to center a specific
> > structure/residue in the box. You can have the output written in the .gro
> > file format, or convert to anything more convenient.
> >
> > With kind regards,
> > ______________________________
> > Kenneth Goossens, PhD student
> > Laboratory of Medicinal Chemistry (Building A - Room 2.13)
> > University of Antwerp - Campus Drie Eiken
> > Universiteitsplein 1
> > B-2610 Wilrijk
> > Belgium
> >
> >
> >
> > ________________________________
> > Van: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> namens Miro Astore <
> > miro.astore at gmail.com>
> > Verzonden: dinsdag 14 januari 2020 3:48
> > Aan: gromacs.org_gmx-users at maillist.sys.kth.se <
> > gromacs.org_gmx-users at maillist.sys.kth.se>
> > Onderwerp: [gmx-users] Loading topology into vmd
> >
> > Hello all,
> >
> > I'm just wondering how people load topologies for systems simulated in
> > gromacs into vmd. It is very annoying to have bonds that aren't in the
> > simulation placed in the visualisation. I'm wondering if anyone has a
> > solution that is easier than simply creating a psf file of the .gro
> system
> > as this can be time consuming for systems with strange geometries.
> >
> > Best, Miro
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

From shlomit.afgin at weizmann.ac.il  Wed Jan 15 09:50:57 2020
From: shlomit.afgin at weizmann.ac.il (Shlomit Afgin)
Date: Wed, 15 Jan 2020 08:50:57 -0000
Subject: [gmx-users] Error:  Cannot find AVX 512F compiler flag
Message-ID: <CBF906C1-9C73-46E7-8D4A-9FC14F8030CF@weizmann.ac.il>


Hi,
I tried to install GROMACS 2019.5 on CentOS7,
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON

I have already installed devtoolset-6 and still get this error:

-- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS
-- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Failed
-- Could not find any flag to build test source (this could be due to either the compiler or binutils)
-- Could not identify number of AVX-512 units - detection program missing compilation prerequisites
-- Could not run code to detect number of AVX-512 FMA units - assuming 2.
-- Detected best SIMD instructions for this CPU - AVX_512
CMake Error at cmake/gmxManageSimd.cmake:51 (message):
  Cannot find AVX 512F compiler flag.  Use a newer compiler, or choose a
  lower level of SIMD (slower).
Call Stack (most recent call first):
  cmake/gmxManageSimd.cmake:186 (gmx_give_fatal_error_when_simd_support_not_found)
  CMakeLists.txt:719 (gmx_manage_simd)


Thanks,
Shlomit

From pall.szilard at gmail.com  Wed Jan 15 10:14:05 2020
From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=)
Date: Wed, 15 Jan 2020 09:14:05 -0000
Subject: [gmx-users] Error: Cannot find AVX 512F compiler flag
In-Reply-To: <CBF906C1-9C73-46E7-8D4A-9FC14F8030CF@weizmann.ac.il>
References: <CBF906C1-9C73-46E7-8D4A-9FC14F8030CF@weizmann.ac.il>
Message-ID: <CANnYEw55zb9uD8j4T7fhhJLh0rNXECZscD30whSpKZNY6H+S4g@mail.gmail.com>

Hi,

What hardware are you targeting? Unless you need AVX512 support, you could
just manually specify the appropriate setting in GMX_SIMD, e.g.
-DGMX_SIMD=AVX2_256 would be appropriate for most cases where AVX512 is not
supported.

Cheers,
--
Szil?rd


On Wed, Jan 15, 2020 at 9:51 AM Shlomit Afgin <shlomit.afgin at weizmann.ac.il>
wrote:

>
> Hi,
> I tried to install GROMACS 2019.5 on CentOS7,
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
>
> I have already installed devtoolset-6 and still get this error:
>
> -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS
> -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Failed
> -- Could not find any flag to build test source (this could be due to
> either the compiler or binutils)
> -- Could not identify number of AVX-512 units - detection program missing
> compilation prerequisites
> -- Could not run code to detect number of AVX-512 FMA units - assuming 2.
> -- Detected best SIMD instructions for this CPU - AVX_512
> CMake Error at cmake/gmxManageSimd.cmake:51 (message):
>   Cannot find AVX 512F compiler flag.  Use a newer compiler, or choose a
>   lower level of SIMD (slower).
> Call Stack (most recent call first):
>   cmake/gmxManageSimd.cmake:186
> (gmx_give_fatal_error_when_simd_support_not_found)
>   CMakeLists.txt:719 (gmx_manage_simd)
>
>
> Thanks,
> Shlomit
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From miro.astore at gmail.com  Wed Jan 15 10:30:20 2020
From: miro.astore at gmail.com (Miro Astore)
Date: Wed, 15 Jan 2020 09:30:20 -0000
Subject: [gmx-users] Loading topology into vmd
In-Reply-To: <CANogp5wFaYi_DFLMU7GiqzZvh+-s9wQbAvf=4NAvmftsyXKQ6A@mail.gmail.com>
References: <CAL3MGYSOEEy70Kp+xCeC6vM1FbzN3SV2oDiuyA7ae+TLc7XgxA@mail.gmail.com>
	<AM0PR01MB65149E6F31C527A89BAFA946F8340@AM0PR01MB6514.eurprd01.prod.exchangelabs.com>
	<CAL3MGYQ1X0EndBb8o1_pVpcBKW6J3QiYEYhEUueB7TtjVYq=nQ@mail.gmail.com>
	<CANogp5wFaYi_DFLMU7GiqzZvh+-s9wQbAvf=4NAvmftsyXKQ6A@mail.gmail.com>
Message-ID: <CAL3MGYQU7npZU4ztiBHfDcKku2Ev7RRraps6BjLkSwG6xU_75w@mail.gmail.com>

This is very helpful thank you. I think I can use this. I will also ask the
vmd mail list.

Best, Miro

Le mer. 15 janv. 2020 ? 19:35, Alessandra Villa <
alessandra.villa.biosim at gmail.com> a ?crit :

> Hi,
> One of the criteria that VMD uses to define bond is distance criteria. When
> you source your gro file, this criteria is applied.
> One way one, I have used is to not visualize  undesired bonds, is the
> following:
> delete the undesired bonds, save the vmd setting (*.vmd file),  load the
> setting before any of the following visualizations.
> That is not the most elegant way, but it works in my case.
> For more elegant ways, you could ask to VMD maillist.
> Best regards
> Alessandra
>
>
> On Tue, Jan 14, 2020 at 8:59 PM Miro Astore <miro.astore at gmail.com> wrote:
>
> > Hi kenny, thanks for getting back to me.
> >
> > I use something similar to what you've suggested to deal with periodic
> > boundary conditions. My current issue is that vmd will place a bond
> between
> > two atoms that are close together in the first frame of the visualization
> > even if those atoms aren't linked in the topology. The fake bonds are
> then
> > kept throughout the visualization . That is, when I load just a gro and a
> > trr.
> >
> > A psf file would fix this situation but my efforts to recreate a whole
> one
> > from my complex system using top2psf.pl hasn't borne much fruit.
> >
> > Just wondering what other people have tried.
> >
> > Best, Miro
> >
> > Le mer. 15 janv. 2020 ? 02:20, Kenny Goossens <
> goossens_kenny at hotmail.com>
> > a ?crit :
> >
> > > Hi,
> > >
> > > I'm not sure what you mean by "bonds that aren't in the simulation",
> but
> > > from my experience, converting your .gro file with gmx trjconv using
> the
> > > -pbc mol and -ur compact options usually gives a clean visualisation.
> If
> > > necessary, you can also use the -center option to center a specific
> > > structure/residue in the box. You can have the output written in the
> .gro
> > > file format, or convert to anything more convenient.
> > >
> > > With kind regards,
> > > ______________________________
> > > Kenneth Goossens, PhD student
> > > Laboratory of Medicinal Chemistry (Building A - Room 2.13)
> > > University of Antwerp - Campus Drie Eiken
> > > Universiteitsplein 1
> > > B-2610 Wilrijk
> > > Belgium
> > >
> > >
> > >
> > > ________________________________
> > > Van: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> > > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> namens Miro Astore
> <
> > > miro.astore at gmail.com>
> > > Verzonden: dinsdag 14 januari 2020 3:48
> > > Aan: gromacs.org_gmx-users at maillist.sys.kth.se <
> > > gromacs.org_gmx-users at maillist.sys.kth.se>
> > > Onderwerp: [gmx-users] Loading topology into vmd
> > >
> > > Hello all,
> > >
> > > I'm just wondering how people load topologies for systems simulated in
> > > gromacs into vmd. It is very annoying to have bonds that aren't in the
> > > simulation placed in the visualisation. I'm wondering if anyone has a
> > > solution that is easier than simply creating a psf file of the .gro
> > system
> > > as this can be time consuming for systems with strange geometries.
> > >
> > > Best, Miro
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

From miro.astore at gmail.com  Wed Jan 15 10:30:20 2020
From: miro.astore at gmail.com (Miro Astore)
Date: Wed, 15 Jan 2020 09:30:20 -0000
Subject: [gmx-users] Loading topology into vmd
In-Reply-To: <CANogp5wFaYi_DFLMU7GiqzZvh+-s9wQbAvf=4NAvmftsyXKQ6A@mail.gmail.com>
References: <CAL3MGYSOEEy70Kp+xCeC6vM1FbzN3SV2oDiuyA7ae+TLc7XgxA@mail.gmail.com>
	<AM0PR01MB65149E6F31C527A89BAFA946F8340@AM0PR01MB6514.eurprd01.prod.exchangelabs.com>
	<CAL3MGYQ1X0EndBb8o1_pVpcBKW6J3QiYEYhEUueB7TtjVYq=nQ@mail.gmail.com>
	<CANogp5wFaYi_DFLMU7GiqzZvh+-s9wQbAvf=4NAvmftsyXKQ6A@mail.gmail.com>
Message-ID: <CAL3MGYQU7npZU4ztiBHfDcKku2Ev7RRraps6BjLkSwG6xU_75w@mail.gmail.com>

This is very helpful thank you. I think I can use this. I will also ask the
vmd mail list.

Best, Miro

Le mer. 15 janv. 2020 ? 19:35, Alessandra Villa <
alessandra.villa.biosim at gmail.com> a ?crit :

> Hi,
> One of the criteria that VMD uses to define bond is distance criteria. When
> you source your gro file, this criteria is applied.
> One way one, I have used is to not visualize  undesired bonds, is the
> following:
> delete the undesired bonds, save the vmd setting (*.vmd file),  load the
> setting before any of the following visualizations.
> That is not the most elegant way, but it works in my case.
> For more elegant ways, you could ask to VMD maillist.
> Best regards
> Alessandra
>
>
> On Tue, Jan 14, 2020 at 8:59 PM Miro Astore <miro.astore at gmail.com> wrote:
>
> > Hi kenny, thanks for getting back to me.
> >
> > I use something similar to what you've suggested to deal with periodic
> > boundary conditions. My current issue is that vmd will place a bond
> between
> > two atoms that are close together in the first frame of the visualization
> > even if those atoms aren't linked in the topology. The fake bonds are
> then
> > kept throughout the visualization . That is, when I load just a gro and a
> > trr.
> >
> > A psf file would fix this situation but my efforts to recreate a whole
> one
> > from my complex system using top2psf.pl hasn't borne much fruit.
> >
> > Just wondering what other people have tried.
> >
> > Best, Miro
> >
> > Le mer. 15 janv. 2020 ? 02:20, Kenny Goossens <
> goossens_kenny at hotmail.com>
> > a ?crit :
> >
> > > Hi,
> > >
> > > I'm not sure what you mean by "bonds that aren't in the simulation",
> but
> > > from my experience, converting your .gro file with gmx trjconv using
> the
> > > -pbc mol and -ur compact options usually gives a clean visualisation.
> If
> > > necessary, you can also use the -center option to center a specific
> > > structure/residue in the box. You can have the output written in the
> .gro
> > > file format, or convert to anything more convenient.
> > >
> > > With kind regards,
> > > ______________________________
> > > Kenneth Goossens, PhD student
> > > Laboratory of Medicinal Chemistry (Building A - Room 2.13)
> > > University of Antwerp - Campus Drie Eiken
> > > Universiteitsplein 1
> > > B-2610 Wilrijk
> > > Belgium
> > >
> > >
> > >
> > > ________________________________
> > > Van: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> > > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> namens Miro Astore
> <
> > > miro.astore at gmail.com>
> > > Verzonden: dinsdag 14 januari 2020 3:48
> > > Aan: gromacs.org_gmx-users at maillist.sys.kth.se <
> > > gromacs.org_gmx-users at maillist.sys.kth.se>
> > > Onderwerp: [gmx-users] Loading topology into vmd
> > >
> > > Hello all,
> > >
> > > I'm just wondering how people load topologies for systems simulated in
> > > gromacs into vmd. It is very annoying to have bonds that aren't in the
> > > simulation placed in the visualisation. I'm wondering if anyone has a
> > > solution that is easier than simply creating a psf file of the .gro
> > system
> > > as this can be time consuming for systems with strange geometries.
> > >
> > > Best, Miro
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

From roland.schulz at intel.com  Wed Jan 15 10:36:31 2020
From: roland.schulz at intel.com (Schulz, Roland)
Date: Wed, 15 Jan 2020 09:36:31 -0000
Subject: [gmx-users] Error:  Cannot find AVX 512F compiler flag
In-Reply-To: <CBF906C1-9C73-46E7-8D4A-9FC14F8030CF@weizmann.ac.il>
References: <CBF906C1-9C73-46E7-8D4A-9FC14F8030CF@weizmann.ac.il>
Message-ID: <BYAPR11MB258192C1841CFE5676AB62B0E0370@BYAPR11MB2581.namprd11.prod.outlook.com>

Are you actually using the GCC from the devtoolset or the default one? Cmake tells you at the very beginning which compiler it is using.

Roland

> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-
> users-bounces at maillist.sys.kth.se> On Behalf Of Shlomit Afgin
> Sent: Wednesday, January 15, 2020 12:51 AM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Error: Cannot find AVX 512F compiler flag
> 
> 
> Hi,
> I tried to install GROMACS 2019.5 on CentOS7, cmake .. -
> DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> 
> I have already installed devtoolset-6 and still get this error:
> 
> -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS
> -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Failed
> -- Could not find any flag to build test source (this could be due to either the
> compiler or binutils)
> -- Could not identify number of AVX-512 units - detection program missing
> compilation prerequisites
> -- Could not run code to detect number of AVX-512 FMA units - assuming 2.
> -- Detected best SIMD instructions for this CPU - AVX_512 CMake Error at
> cmake/gmxManageSimd.cmake:51 (message):
>   Cannot find AVX 512F compiler flag.  Use a newer compiler, or choose a
>   lower level of SIMD (slower).
> Call Stack (most recent call first):
>   cmake/gmxManageSimd.cmake:186
> (gmx_give_fatal_error_when_simd_support_not_found)
>   CMakeLists.txt:719 (gmx_manage_simd)
> 
> 
> Thanks,
> Shlomit
> --
> Gromacs Users mailing list
> 
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
> mail to gmx-users-request at gromacs.org.

From shlomit.afgin at weizmann.ac.il  Wed Jan 15 10:45:00 2020
From: shlomit.afgin at weizmann.ac.il (Shlomit Afgin)
Date: Wed, 15 Jan 2020 09:45:00 -0000
Subject: [gmx-users] Error: Cannot find AVX 512F compiler flag
In-Reply-To: <CANnYEw55zb9uD8j4T7fhhJLh0rNXECZscD30whSpKZNY6H+S4g@mail.gmail.com>
References: <CBF906C1-9C73-46E7-8D4A-9FC14F8030CF@weizmann.ac.il>
	<CANnYEw55zb9uD8j4T7fhhJLh0rNXECZscD30whSpKZNY6H+S4g@mail.gmail.com>
Message-ID: <8806AC21-F166-46FF-9926-6F44C5CDA7BD@weizmann.ac.il>



I ran:

cat /proc/cpuinfo | grep -i avx512



and got:

avx512f avx512dq avx512cd avx512bw avx512vl



So I thought I can use it. Am I wrong?



Shlomit



?On 15/01/2020, 11:14, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Szil?rd P?ll" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of pall.szilard at gmail.com> wrote:



    Hi,



    What hardware are you targeting? Unless you need AVX512 support, you could

    just manually specify the appropriate setting in GMX_SIMD, e.g.

    -DGMX_SIMD=AVX2_256 would be appropriate for most cases where AVX512 is not

    supported.



    Cheers,

    --

    Szil?rd





    On Wed, Jan 15, 2020 at 9:51 AM Shlomit Afgin <shlomit.afgin at weizmann.ac.il>

    wrote:



    >

    > Hi,

    > I tried to install GROMACS 2019.5 on CentOS7,

    > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON

    >

    > I have already installed devtoolset-6 and still get this error:

    >

    > -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS

    > -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Failed

    > -- Could not find any flag to build test source (this could be due to

    > either the compiler or binutils)

    > -- Could not identify number of AVX-512 units - detection program missing

    > compilation prerequisites

    > -- Could not run code to detect number of AVX-512 FMA units - assuming 2.

    > -- Detected best SIMD instructions for this CPU - AVX_512

    > CMake Error at cmake/gmxManageSimd.cmake:51 (message):

    >   Cannot find AVX 512F compiler flag.  Use a newer compiler, or choose a

    >   lower level of SIMD (slower).

    > Call Stack (most recent call first):

    >   cmake/gmxManageSimd.cmake:186

    > (gmx_give_fatal_error_when_simd_support_not_found)

    >   CMakeLists.txt:719 (gmx_manage_simd)

    >

    >

    > Thanks,

    > Shlomit

    > --

    > Gromacs Users mailing list

    >

    > * Please search the archive at

    > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

    > posting!

    >

    > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

    >

    > * For (un)subscribe requests visit

    > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or

    > send a mail to gmx-users-request at gromacs.org.

    >

    --

    Gromacs Users mailing list



    * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!



    * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists



    * For (un)subscribe requests visit

    https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

From tru at pasteur.fr  Wed Jan 15 11:06:58 2020
From: tru at pasteur.fr (Tru Huynh)
Date: Wed, 15 Jan 2020 10:06:58 -0000
Subject: [gmx-users] Error:  Cannot find AVX 512F compiler flag
In-Reply-To: <CBF906C1-9C73-46E7-8D4A-9FC14F8030CF@weizmann.ac.il>
References: <CBF906C1-9C73-46E7-8D4A-9FC14F8030CF@weizmann.ac.il>
Message-ID: <20200115100652.GO7760@sillage.bis.pasteur.fr>

On Wed, Jan 15, 2020 at 08:50:46AM +0000, Shlomit Afgin wrote:
> 
> Hi,
> I tried to install GROMACS 2019.5 on CentOS7,
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> 
> I have already installed devtoolset-6 and still get this error:
installed, but not using it?

[tru at elitebook840g3 ~]$ type gcc
gcc is /usr/bin/gcc
[tru at elitebook840g3 ~]$ scl enable devtoolset-6 bash
[tru at elitebook840g3 ~]$ type gcc
gcc is /opt/rh/devtoolset-6/root/usr/bin/gcc

Tru

-- 
Tru Huynh (PhD) | mailto:tru at pasteur.fr | tel +33 1 45 68 87 37
https://research.pasteur.fr/en/team/structural-bioinformatics/
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France  

From mark.j.abraham at gmail.com  Wed Jan 15 11:17:54 2020
From: mark.j.abraham at gmail.com (Mark Abraham)
Date: Wed, 15 Jan 2020 10:17:54 -0000
Subject: [gmx-users] Error: Cannot find AVX 512F compiler flag
In-Reply-To: <20200115100652.GO7760@sillage.bis.pasteur.fr>
References: <CBF906C1-9C73-46E7-8D4A-9FC14F8030CF@weizmann.ac.il>
	<20200115100652.GO7760@sillage.bis.pasteur.fr>
Message-ID: <CAMNuMAS9uu_jNi=kfkd-AdkG3DhT1MqPaexGiUQX3S0WhUmS6g@mail.gmail.com>

On Wed, 15 Jan 2020 at 11:07, Tru Huynh <tru at pasteur.fr> wrote:

>
> gcc is /opt/rh/devtoolset-6/root/usr/bin/gcc
>

Good, so is Cmake using it? (e.g. remove the build dir and run cmake again
to see what it first reports, or inspect $builddir/CMakeCache.txt for the
compiler setting)

Mark

From ashmakhan200 at gmail.com  Wed Jan 15 11:21:06 2020
From: ashmakhan200 at gmail.com (Ashma Khan)
Date: Wed, 15 Jan 2020 10:21:06 -0000
Subject: [gmx-users] Regarding high RMSD
Message-ID: <CAG89CR5WTg2cd7H-JQuOsGmQ4WeEhLdM6V2Ux+1eA+YEm7KEgQ@mail.gmail.com>

Dear all,
I have calculated the c-alpha RMSD of dimer having 7 residues peptide each
by using command gmx rms. But the calculated RMSD 14 Angstorm is very high,
although I have applied all pbc conditions. Anybody can suggest me why so
much high RMSD is coming or is it possible.

-- 
Ashma Khan
Research Scholar
Department of Chemistry
AMU, Aligarh

From sadafrani6 at gmail.com  Wed Jan 15 11:37:14 2020
From: sadafrani6 at gmail.com (Sadaf Rani)
Date: Wed, 15 Jan 2020 10:37:14 -0000
Subject: [gmx-users] Fwd: A list of missing interactions
In-Reply-To: <CAH9Uu9PfmNEdMs1gx7iQ0Oz6R98z+guMNDqMsHz2VD0k6YpRLw@mail.gmail.com>
References: <CAH9Uu9PfmNEdMs1gx7iQ0Oz6R98z+guMNDqMsHz2VD0k6YpRLw@mail.gmail.com>
Message-ID: <CAH9Uu9O3kENMgiKxDRFfj1ie5WZLCJUzoPorwA_LrUvPvHKV0Q@mail.gmail.com>

Dear Gromacs users
I am facing this error during free energy calculation of protein-ligand for
which I have applied restrained to some atoms of protein residue and
ligand.
A list of missing interactions:
      Restraint Pot. of      1 missing      1

Molecule type 'Protein'
the first 10 missing interactions, except for exclusions:
      Restraint Pot. atoms 3437 7908           global  3437  7908

-------------------------------------------------------
Program:     gmx mdrun, version 2018.1
Source file: src/gromacs/domdec/domdec_topology.cpp (line 436)
MPI rank:    0 (out of 2)

Fatal error:
1 of the 64584 bonded interactions could not be calculated because some
atoms
involved moved further apart than the multi-body cut-off distance (4.47682
nm)
or the two-body cut-off distance (4.47682 nm), see option -rdd, for pairs
and
tabulated bonds also see option -ddcheck

Could anybody please suggest how should I fix this error? I would be really
thankful.

Regards

Sadaf

From gmx.user88 at gmail.com  Wed Jan 15 12:32:45 2020
From: gmx.user88 at gmail.com (gmx user1)
Date: Wed, 15 Jan 2020 11:32:45 -0000
Subject: [gmx-users] Umbrella sampling with restraint on the center of mass
	of ligand
Message-ID: <CAAqsoymGj_gxvk-DpVhw6UNMULNyHG2PS-+0grDcBcE7Y8DnZQ@mail.gmail.com>

Dear GMX users

I am doing umbrella sampling to obtain a PMF relative to the translocation
of a ligand within a membrane protein.
I want to add an harmonic potential to restrain the center of mass of the
ligand in each window ,
similarly to the protocols used by Subramanian et al (
https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.8b00624 ;
https://www.sciencedirect.com/science/article/pii/S0005273615004319?via%3Dihub
)

Yet, I am not certain of which .mdp settings I should use to accomplish my
goal, the documentation is not clear and most infomation I find
refers to the application of harmonic potentials when the reaction
coordinate is a distance between two groups.

Here are my .mdp settings:

pull                    = yes
pull_print_com          = yes
pull_print_ref_value    = yes
pull_nstxout            = 500
pull_nstfout            = 0
pull_ncoords            = 1         ; only one reaction coordinate
pull_ngroups            = 1
pull_coord1_geometry    = direction-periodic
pull_coord1_vec         = 0 0 1
pull-coord1-origin      = 0 0 0
pull_group1_name        = LIG
pull_coord1_groups      = 0 1
pull_coord1_type        = umbrella  ; harmonic potential
pull_coord1_start       = yes       ; define initial COM distance > 0
pull_coord1_rate        = 0.0       ; restrain in place
pull_coord1_k           = 500      ; kJ mol^-1 nm^-2

Essentially, I created a vector between the center-of-mass of the ligand
and an absolute reference (0,0,0) and I had to use pull_coord1_geometry =
direction-periodic ( instead of direction) ,because the simulation crashed.
This also forces me to perform an NVE simulation.

Is this the right way of applying a an harmonic restraint on the
center-of-mass of a ligand for umbrella sampling? Are these settings
correct?

Any help is appreaciated.

Thanks in advance

From akash.pandya.15 at ucl.ac.uk  Wed Jan 15 17:58:34 2020
From: akash.pandya.15 at ucl.ac.uk (Pandya, Akash)
Date: Wed, 15 Jan 2020 16:58:34 -0000
Subject: [gmx-users] Hydrogen bonding criteria in Gromacs
Message-ID: <DB6PR0101MB2424708E45DFBC1D054F3E52EB370@DB6PR0101MB2424.eurprd01.prod.exchangelabs.com>

Hi all,

I  wanted to ask a couple of questions about the hydrogen bonding calculation in Gromacs.


  1.   Why is the default angle cutoff 30 degrees? The reason I ask this is because I?ve seen in other packages with higher angle cutoffs.
  2.  What?s the best way to define cutoffs for my system? I know this is ambiguous, but is there a procedure I can use to decide?

Any guidance will be much appreciated.

Thank you,

Akash

Get Outlook for iOS<https://aka.ms/o0ukef>

From vuqv.phys at gmail.com  Wed Jan 15 18:21:55 2020
From: vuqv.phys at gmail.com (Quyen V. Vu)
Date: Wed, 15 Jan 2020 17:21:55 -0000
Subject: [gmx-users] Hydrogen bonding criteria in Gromacs
In-Reply-To: <DB6PR0101MB2424708E45DFBC1D054F3E52EB370@DB6PR0101MB2424.eurprd01.prod.exchangelabs.com>
References: <DB6PR0101MB2424708E45DFBC1D054F3E52EB370@DB6PR0101MB2424.eurprd01.prod.exchangelabs.com>
Message-ID: <CA+CKAfxWMs88rK9tU9kW+UGSSqwRHtxohzWZV4Nzb_qV82CjgQ@mail.gmail.com>

Hydrogen bonding is approximated by charge-dipole interaction, which is
very orientation-sensitive, the energy of this kind interactions
are proportional to the cosine of the angle.
https://en.wikibooks.org/wiki/Molecular_Simulation/Charge-Dipole_Interactions



On Wed, Jan 15, 2020 at 5:59 PM Pandya, Akash <akash.pandya.15 at ucl.ac.uk>
wrote:

> Hi all,
>
> I  wanted to ask a couple of questions about the hydrogen bonding
> calculation in Gromacs.
>
>
>   1.   Why is the default angle cutoff 30 degrees? The reason I ask this
> is because I?ve seen in other packages with higher angle cutoffs.
>   2.  What?s the best way to define cutoffs for my system? I know this is
> ambiguous, but is there a procedure I can use to decide?
>
> Any guidance will be much appreciated.
>
> Thank you,
>
> Akash
>
> Get Outlook for iOS<https://aka.ms/o0ukef>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From jalemkul at vt.edu  Wed Jan 15 18:26:00 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Wed, 15 Jan 2020 17:26:00 -0000
Subject: [gmx-users] Query regarding do_dssp program
In-Reply-To: <CACgG5G8SsEKvZJ7SGmDUd61scjv+A6LOrM3RWAs1bjxa2Ewnkw@mail.gmail.com>
References: <CACgG5G_W98HHjQOVfcExjW09-4-93XRCChf5n8Hk6hYsY-XP4g@mail.gmail.com>
	<CANogp5yG74V8SU9o6h4q4NT3P7=vc7r29fXo9PTGym_w5uMS-w@mail.gmail.com>
	<CACgG5G-upuHz8NV9ggCZo08eyzdYXm6n9SYt=daVTw5Y9z2Tug@mail.gmail.com>
	<5725d611-97f4-ef09-4ee6-acc151e87884@vt.edu>
	<CACgG5G8bsFiXd13gxVyLFbQb9XQg+GkC6nXP9Kbw_uXJrGTiMA@mail.gmail.com>
	<a8c319c9-dc32-afec-a96c-9dd2e843039a@vt.edu>
	<CACgG5G8SsEKvZJ7SGmDUd61scjv+A6LOrM3RWAs1bjxa2Ewnkw@mail.gmail.com>
Message-ID: <ad8d8256-f8ee-fa24-786f-2afc2d89bd02@vt.edu>



On 1/15/20 12:27 AM, Sundari wrote:
> I tried all the options.. I load gro file instead of xtc. At zero frame I
> gave representations new cartoon + secondary structure.. then I calculate
> sec str details by going on vmd timeline.
> I don't know what I am missing.. I am doing the same which I used all the
> time.
> Because these are two totally different secondary structures that's why I
> was worrying.. because these are major structures one reports so Very
> important to resolve this issue.

Without access to the coordinate file, there's nothing I can tell you. 
If you want to send me that snapshot off-list, I can probably take a 
quick look and see if I can get to the bottom of it.

-Justin

> On Wednesday, January 15, 2020, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 1/13/20 9:15 AM, Sundari wrote:
>>
>>> Yes, Sir,  I  made the gro file for a particular time by using "gmx
>>> trjconv" command ( also checked with -pbc mol, whole, no_jump options )
>>> but every time the 2ndary structure visualization in vmd is different from
>>> dssp sequence of residues in gromacs. Fox example in my protein dssp shows
>>> 8 residues making beta-sheets but when I load that particular time frame
>>> in
>>> vmd for visualizing the structure,  these 8 residues showing 5-helix
>>> structure.
>>>
>>> Please suggest something.
>>>
>> I'm afraid I can't. Those are two completely different hydrogen bonding
>> patterns and I can't imagine how the algorithms would differ so
>> dramatically. I have seen VMD render coils for helices and sheets but never
>> a totally different secondary structure. Be sure you're telling VMD to
>> re-compute structures and re-color the secondary structure elements at
>> every snapshot for trajectory visualization, otherwise it will render
>> everything the same as the initial frame, which will obviously be wrong in
>> the case of large structural changes.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From jalemkul at vt.edu  Wed Jan 15 18:28:11 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Wed, 15 Jan 2020 17:28:11 -0000
Subject: [gmx-users] Umbrella sampling with restraint on the center of
 mass of ligand
In-Reply-To: <CAAqsoymGj_gxvk-DpVhw6UNMULNyHG2PS-+0grDcBcE7Y8DnZQ@mail.gmail.com>
References: <CAAqsoymGj_gxvk-DpVhw6UNMULNyHG2PS-+0grDcBcE7Y8DnZQ@mail.gmail.com>
Message-ID: <608bb525-a66f-e3b0-fe8c-f6d2844f40f0@vt.edu>



On 1/15/20 6:32 AM, gmx user1 wrote:
> Dear GMX users
>
> I am doing umbrella sampling to obtain a PMF relative to the translocation
> of a ligand within a membrane protein.
> I want to add an harmonic potential to restrain the center of mass of the
> ligand in each window ,
> similarly to the protocols used by Subramanian et al (
> https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.8b00624 ;
> https://www.sciencedirect.com/science/article/pii/S0005273615004319?via%3Dihub
> )
>
> Yet, I am not certain of which .mdp settings I should use to accomplish my
> goal, the documentation is not clear and most infomation I find
> refers to the application of harmonic potentials when the reaction
> coordinate is a distance between two groups.

If you're not clear what the published method is or how to reproduce it, 
I suggest you contact the corresponding author and ask for sample input 
files.

> Here are my .mdp settings:
>
> pull                    = yes
> pull_print_com          = yes
> pull_print_ref_value    = yes
> pull_nstxout            = 500
> pull_nstfout            = 0
> pull_ncoords            = 1         ; only one reaction coordinate
> pull_ngroups            = 1
> pull_coord1_geometry    = direction-periodic
> pull_coord1_vec         = 0 0 1
> pull-coord1-origin      = 0 0 0
> pull_group1_name        = LIG
> pull_coord1_groups      = 0 1
> pull_coord1_type        = umbrella  ; harmonic potential
> pull_coord1_start       = yes       ; define initial COM distance > 0
> pull_coord1_rate        = 0.0       ; restrain in place
> pull_coord1_k           = 500      ; kJ mol^-1 nm^-2
>
> Essentially, I created a vector between the center-of-mass of the ligand
> and an absolute reference (0,0,0) and I had to use pull_coord1_geometry =
> direction-periodic ( instead of direction) ,because the simulation crashed.
> This also forces me to perform an NVE simulation.
>
> Is this the right way of applying a an harmonic restraint on the
> center-of-mass of a ligand for umbrella sampling? Are these settings
> correct?

If you're looking at ligand translocation across a membrane, you should 
not be using (0,0,0) as a reference. The conventional reaction 
coordinate is the normal to the bilayer, so the reaction coordinate 
connects the COM of the bilayer with the COM of the ligand along the z-axis.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From jalemkul at vt.edu  Wed Jan 15 18:29:51 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Wed, 15 Jan 2020 17:29:51 -0000
Subject: [gmx-users] Hydrogen bonding criteria in Gromacs
In-Reply-To: <DB6PR0101MB2424708E45DFBC1D054F3E52EB370@DB6PR0101MB2424.eurprd01.prod.exchangelabs.com>
References: <DB6PR0101MB2424708E45DFBC1D054F3E52EB370@DB6PR0101MB2424.eurprd01.prod.exchangelabs.com>
Message-ID: <e846b411-71ae-1a7a-2936-7ed5f757fdc7@vt.edu>



On 1/15/20 11:57 AM, Pandya, Akash wrote:
> Hi all,
>
> I  wanted to ask a couple of questions about the hydrogen bonding calculation in Gromacs.
>
>
>    1.   Why is the default angle cutoff 30 degrees? The reason I ask this is because I?ve seen in other packages with higher angle cutoffs.

It depends on how the software defines the angle. The GROMACS convention 
is the angle corresponds to H-D-A rather than D-H-A like some other 
programs. H-D-A cutoff of 30 degrees is equivalent to the "conventional" 
150-degree D-H-A cutoff.

>    2.  What?s the best way to define cutoffs for my system? I know this is ambiguous, but is there a procedure I can use to decide?

The default criteria are widely used and usually don't require any tuning.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From alexanderwien2k at gmail.com  Wed Jan 15 19:10:59 2020
From: alexanderwien2k at gmail.com (Alex)
Date: Wed, 15 Jan 2020 18:10:59 -0000
Subject: [gmx-users] gmx genconf
Message-ID: <CAEDv6u5V6_4vtyAiNBQpyxWZaFUB5Un_qjFg1HaqEHa7QTejWg@mail.gmail.com>

Dear all,
I am aware of the "gmx genconf -f time.gro -nbox 2 2 2 -o 2times.gro" in
order to expand a gro file 2 times in all directions. I wonder if it is
possible to expand a xtc trajectory and outpout a larger trajectory in the
same way?

According to genconf man page I see that the input could be -trj.xtc, but
no trajectory as output has been mentioned there apparently.

Regards,
Alex

From 272699575 at qq.com  Wed Jan 15 20:39:03 2020
From: 272699575 at qq.com (=?gb18030?B?WkhBTkcgQ2hlbmc=?=)
Date: Wed, 15 Jan 2020 19:39:03 -0000
Subject: [gmx-users] Why it is run so slow in gromacs 2019.3 compared to
	VERSION 5.1.1?
Message-ID: <tencent_B72778E0898ACC0EDEE547065FCEEEA11706@qq.com>

I have a nearly identical run using the "VERSION 2019.3" compared to my previous "VERSION 5.1.1". Everything during the preparation is the same except "-r" needs to be added in the "VERSION 2019.3". So "-r em.gro", "-r nvt.gro" and "-r npt.gro" are added in the grompp commands for NVT, NPT and production run, respectively.


Using "-pe mpi 12" (i.e. 12 nodes) per hour, only 5-7 ps can be processed in the "VERSION 2019.3", while 200 ps can be achieved in the "VERSION 5.1.1". Can I ask is this normal? Is there some configuration I can do in the "VERSION 2019.3" so as to accelerate the MD?&nbsp;


I follow Justin's tutorial at http://www.mdtutorials.com/gmx/lysozyme/index.html
The commands I used are listed below.


gmx pdb2gmx&nbsp; -f Fab.pdb -o Fab_processed.gro -water spce&nbsp; -inter&nbsp; -ignh -merge interactive
gmx editconf -f Fab_processed.gro -o Fab_newbox.gro -c -d 1.0 -bt cubic
gmx solvate -cp Fab_newbox.gro -cs spc216.gro -o Fab_solv.gro -p topol.top
gmx grompp -f ions.mdp -c Fab_solv.gro -p topol.top -o ions.tpr -maxwarn 1&nbsp;
gmx genion -s ions.tpr -o Fab_solv_ions.gro -p topol.top -pname NA -nname CL -nn 31 -neutral -conc 0.05
(Afterwards, using the HPC to run)
gmx grompp -f minim.mdp -c Fab_solv_ions.gro -p topol.top -o em.tpr
gerun mdrun_mpi -v -deffnm em
gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -r em.gro
gerun mdrun_mpi -deffnm nvt
gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -r nvt.gro
gerun mdrun_mpi -deffnm npt
gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -r npt.gro
gmx mdrun -deffnm md_0_1 -cpi -append

From marcelodepolo at gmail.com  Wed Jan 15 20:39:10 2020
From: marcelodepolo at gmail.com (=?UTF-8?Q?Marcelo_Dep=C3=B3lo?=)
Date: Wed, 15 Jan 2020 19:39:10 -0000
Subject: [gmx-users] cmaptypes format
Message-ID: <CAFAAhpZfQqwizYca8PvaeyB-0Qp+gHFCu9ZsW_v5J_fwKR+3AQ@mail.gmail.com>

Hi everyone!

I was wondering about the cmaptypes format within cmap.itp file.

[ cmaptypes ]
C N CT C N 1 24 24\

I understand that C-N-CT-C = phi, N-CT-C-N = psi and 24x24 is the grid
size. What does this '1' mean?

Thanks in advance!
--
Marcelo Dep?lo Pol?to
Postdoctoral Researcher
BIOAGRO - Room T07
Department of General Biology - UFV
Contact: + 55 31 3612-2464

From jalemkul at vt.edu  Wed Jan 15 22:47:40 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Wed, 15 Jan 2020 21:47:40 -0000
Subject: [gmx-users] Why it is run so slow in gromacs 2019.3 compared to
 VERSION 5.1.1?
In-Reply-To: <tencent_B72778E0898ACC0EDEE547065FCEEEA11706@qq.com>
References: <tencent_B72778E0898ACC0EDEE547065FCEEEA11706@qq.com>
Message-ID: <863627d6-ae63-0867-4dc9-9930d44ed21b@vt.edu>



On 1/15/20 2:38 PM, ZHANG Cheng wrote:
> I have a nearly identical run using the "VERSION 2019.3" compared to my previous "VERSION 5.1.1". Everything during the preparation is the same except "-r" needs to be added in the "VERSION 2019.3". So "-r em.gro", "-r nvt.gro" and "-r npt.gro" are added in the grompp commands for NVT, NPT and production run, respectively.
>
>
> Using "-pe mpi 12" (i.e. 12 nodes) per hour, only 5-7 ps can be processed in the "VERSION 2019.3", while 200 ps can be achieved in the "VERSION 5.1.1". Can I ask is this normal? Is there some configuration I can do in the "VERSION 2019.3" so as to accelerate the MD?&nbsp;
>
>
> I follow Justin's tutorial at http://www.mdtutorials.com/gmx/lysozyme/index.html
> The commands I used are listed below.
>
>
> gmx pdb2gmx&nbsp; -f Fab.pdb -o Fab_processed.gro -water spce&nbsp; -inter&nbsp; -ignh -merge interactive
> gmx editconf -f Fab_processed.gro -o Fab_newbox.gro -c -d 1.0 -bt cubic
> gmx solvate -cp Fab_newbox.gro -cs spc216.gro -o Fab_solv.gro -p topol.top
> gmx grompp -f ions.mdp -c Fab_solv.gro -p topol.top -o ions.tpr -maxwarn 1&nbsp;
> gmx genion -s ions.tpr -o Fab_solv_ions.gro -p topol.top -pname NA -nname CL -nn 31 -neutral -conc 0.05
> (Afterwards, using the HPC to run)
> gmx grompp -f minim.mdp -c Fab_solv_ions.gro -p topol.top -o em.tpr
> gerun mdrun_mpi -v -deffnm em
> gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -r em.gro
> gerun mdrun_mpi -deffnm nvt
> gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -r nvt.gro
> gerun mdrun_mpi -deffnm npt
> gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -r npt.gro
> gmx mdrun -deffnm md_0_1 -cpi -append

Performance metrics are reported in the .log file from the run. Check 
there to see what is happening.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From jalemkul at vt.edu  Wed Jan 15 22:47:59 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Wed, 15 Jan 2020 21:47:59 -0000
Subject: [gmx-users] cmaptypes format
In-Reply-To: <CAFAAhpZfQqwizYca8PvaeyB-0Qp+gHFCu9ZsW_v5J_fwKR+3AQ@mail.gmail.com>
References: <CAFAAhpZfQqwizYca8PvaeyB-0Qp+gHFCu9ZsW_v5J_fwKR+3AQ@mail.gmail.com>
Message-ID: <b4a3ab9f-8f3e-8407-a9d9-3f93588fb4a2@vt.edu>



On 1/15/20 2:38 PM, Marcelo Dep?lo wrote:
> Hi everyone!
>
> I was wondering about the cmaptypes format within cmap.itp file.
>
> [ cmaptypes ]
> C N CT C N 1 24 24\
>
> I understand that C-N-CT-C = phi, N-CT-C-N = psi and 24x24 is the grid
> size. What does this '1' mean?

Probably a useless/dummy function type.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From 272699575 at qq.com  Thu Jan 16 00:59:26 2020
From: 272699575 at qq.com (=?ISO-8859-1?B?WkhBTkcgQ2hlbmc=?=)
Date: Wed, 15 Jan 2020 23:59:26 -0000
Subject: [gmx-users] Why it is run so slow in gromacs 2019.3 compared to
	VERSION 5.1.1?
In-Reply-To: <tencent_B72778E0898ACC0EDEE547065FCEEEA11706@qq.com>
References: <tencent_B72778E0898ACC0EDEE547065FCEEEA11706@qq.com>
Message-ID: <tencent_272F50F0AE937B99023CA48F383E81DD3607@qq.com>

Hi Justin, what kind of information should I look at in the log files? They are too big to paste here. Would it be possible if you can see them at&nbsp;https://github.com/lanselibai/gromacs-20200115&nbsp;?


Thank you!


------------------&nbsp;Original&nbsp;------------------
From:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
Date:&nbsp;Thu, Jan 16, 2020 03:38 AM
To:&nbsp;"gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se&gt;;
Cc:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
Subject:&nbsp;Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?



I have a nearly identical run using the "VERSION 2019.3" compared to my previous "VERSION 5.1.1". Everything during the preparation is the same except "-r" needs to be added in the "VERSION 2019.3". So "-r em.gro", "-r nvt.gro" and "-r npt.gro" are added in the grompp commands for NVT, NPT and production run, respectively.


Using "-pe mpi 12" (i.e. 12 nodes) per hour, only 5-7 ps can be processed in the "VERSION 2019.3", while 200 ps can be achieved in the "VERSION 5.1.1". Can I ask is this normal? Is there some configuration I can do in the "VERSION 2019.3" so as to accelerate the MD? 


I follow Justin's tutorial at http://www.mdtutorials.com/gmx/lysozyme/index.html
The commands I used are listed below.


gmx pdb2gmx&nbsp; -f Fab.pdb -o Fab_processed.gro -water spce&nbsp; -inter&nbsp; -ignh -merge interactive
gmx editconf -f Fab_processed.gro -o Fab_newbox.gro -c -d 1.0 -bt cubic
gmx solvate -cp Fab_newbox.gro -cs spc216.gro -o Fab_solv.gro -p topol.top
gmx grompp -f ions.mdp -c Fab_solv.gro -p topol.top -o ions.tpr -maxwarn 1 
gmx genion -s ions.tpr -o Fab_solv_ions.gro -p topol.top -pname NA -nname CL -nn 31 -neutral -conc 0.05
(Afterwards, using the HPC to run)
gmx grompp -f minim.mdp -c Fab_solv_ions.gro -p topol.top -o em.tpr
gerun mdrun_mpi -v -deffnm em
gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -r em.gro
gerun mdrun_mpi -deffnm nvt
gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -r nvt.gro
gerun mdrun_mpi -deffnm npt
gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -r npt.gro
gmx mdrun -deffnm md_0_1 -cpi -append

From jalemkul at vt.edu  Thu Jan 16 01:03:50 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Thu, 16 Jan 2020 00:03:50 -0000
Subject: [gmx-users] Why it is run so slow in gromacs 2019.3 compared to
 VERSION 5.1.1?
In-Reply-To: <tencent_272F50F0AE937B99023CA48F383E81DD3607@qq.com>
References: <tencent_B72778E0898ACC0EDEE547065FCEEEA11706@qq.com>
	<tencent_272F50F0AE937B99023CA48F383E81DD3607@qq.com>
Message-ID: <502777f1-3bf8-d951-9541-8a9fd0e0c6af@vt.edu>



On 1/15/20 6:58 PM, ZHANG Cheng wrote:
> Hi Justin, what kind of information should I look at in the log files? They are too big to paste here. Would it be possible if you can see them at&nbsp;https://github.com/lanselibai/gromacs-20200115&nbsp;?

It doesn't look like either of those runs actually finished, and you 
have very frequent restarts from checkpoint files, so I don't see 
performance statistics. Relevant information will be printed in an 
obvious summary at the end of the output.

Try running a very short simulation with each version that runs to 
completion and look at the end of the .log file.

Also note that at least in version 5.1, you are not compiling GROMACS 
for maximum performance.

-Justin

>
> Thank you!
>
>
> ------------------&nbsp;Original&nbsp;------------------
> From:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
> Date:&nbsp;Thu, Jan 16, 2020 03:38 AM
> To:&nbsp;"gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se&gt;;
> Cc:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
> Subject:&nbsp;Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?
>
>
>
> I have a nearly identical run using the "VERSION 2019.3" compared to my previous "VERSION 5.1.1". Everything during the preparation is the same except "-r" needs to be added in the "VERSION 2019.3". So "-r em.gro", "-r nvt.gro" and "-r npt.gro" are added in the grompp commands for NVT, NPT and production run, respectively.
>
>
> Using "-pe mpi 12" (i.e. 12 nodes) per hour, only 5-7 ps can be processed in the "VERSION 2019.3", while 200 ps can be achieved in the "VERSION 5.1.1". Can I ask is this normal? Is there some configuration I can do in the "VERSION 2019.3" so as to accelerate the MD?
>
>
> I follow Justin's tutorial at http://www.mdtutorials.com/gmx/lysozyme/index.html
> The commands I used are listed below.
>
>
> gmx pdb2gmx&nbsp; -f Fab.pdb -o Fab_processed.gro -water spce&nbsp; -inter&nbsp; -ignh -merge interactive
> gmx editconf -f Fab_processed.gro -o Fab_newbox.gro -c -d 1.0 -bt cubic
> gmx solvate -cp Fab_newbox.gro -cs spc216.gro -o Fab_solv.gro -p topol.top
> gmx grompp -f ions.mdp -c Fab_solv.gro -p topol.top -o ions.tpr -maxwarn 1
> gmx genion -s ions.tpr -o Fab_solv_ions.gro -p topol.top -pname NA -nname CL -nn 31 -neutral -conc 0.05
> (Afterwards, using the HPC to run)
> gmx grompp -f minim.mdp -c Fab_solv_ions.gro -p topol.top -o em.tpr
> gerun mdrun_mpi -v -deffnm em
> gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -r em.gro
> gerun mdrun_mpi -deffnm nvt
> gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -r nvt.gro
> gerun mdrun_mpi -deffnm npt
> gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -r npt.gro
> gmx mdrun -deffnm md_0_1 -cpi -append

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From myunggi at pukyong.ac.kr  Thu Jan 16 04:06:17 2020
From: myunggi at pukyong.ac.kr (Myunggi Yi)
Date: Thu, 16 Jan 2020 03:06:17 -0000
Subject: [gmx-users] Hydrogen bonding criteria in Gromacs
In-Reply-To: <e846b411-71ae-1a7a-2936-7ed5f757fdc7@vt.edu>
References: <DB6PR0101MB2424708E45DFBC1D054F3E52EB370@DB6PR0101MB2424.eurprd01.prod.exchangelabs.com>
	<e846b411-71ae-1a7a-2936-7ed5f757fdc7@vt.edu>
Message-ID: <CAHXfRVNQ0Kg-8LqqtSFkx0kjYB=gB7x2o8v0N1q_KnSLkHCZ2Q@mail.gmail.com>

Dear Dr. Justin Lemkul,

Can you explain why the D-H-A is 150?

If H-D-A is 30, then D-H-A should be smaller than 150 degrees.
Since the sum of interior angles of a triangle should be 180 degrees...
See the following triangle.

                     H

D                                                           A


Am I missing something?


On Thu, Jan 16, 2020 at 2:30 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/15/20 11:57 AM, Pandya, Akash wrote:
> > Hi all,
> >
> > I  wanted to ask a couple of questions about the hydrogen bonding
> calculation in Gromacs.
> >
> >
> >    1.   Why is the default angle cutoff 30 degrees? The reason I ask
> this is because I?ve seen in other packages with higher angle cutoffs.
>
> It depends on how the software defines the angle. The GROMACS convention
> is the angle corresponds to H-D-A rather than D-H-A like some other
> programs. H-D-A cutoff of 30 degrees is equivalent to the "conventional"
> 150-degree D-H-A cutoff.
>
> >    2.  What?s the best way to define cutoffs for my system? I know this
> is ambiguous, but is there a procedure I can use to decide?
>
> The default criteria are widely used and usually don't require any tuning.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From dkozuch at princeton.edu  Thu Jan 16 04:51:57 2020
From: dkozuch at princeton.edu (Daniel Kozuch)
Date: Thu, 16 Jan 2020 03:51:57 -0000
Subject: [gmx-users] Lambda Weights from Expanded Ensemble Code
Message-ID: <CAOKxWzJb8aUpQD5f6s_hAXp7cUOivRrO_BShJPxTWcuGnH9kQA@mail.gmail.com>

Hello,

I am interested in using simulated tempering in GROMACS (2019.5) under the
expanded ensemble options. Is there a way to monitor the ensemble weights
as the simulation progresses? I think in theory they are supposed to be
printed out in the log file, but it is only printing 0, -nan, and inf:

            MC-lambda information
  N  Temp.(K)    Count   G(in kT)  dG(in kT)
...
 36  359.105      118       -nan       -nan <<
 37  366.880       96       -nan       -nan
 38  374.852      107       -nan       -nan
 39  383.026      129       -nan       -nan
 40  391.407      166       -nan       -nan
 41  400.000      199       -nan    0.00000

Here are my relevant mdp settings:
simulated-tempering             = yes
nstexpanded                     = 500
simulated-tempering-scaling     = exponential
lmc-stats                       = metropolis-transition
lmc-move                        = metropolis

Any suggestions?

Best,
Dan Kozuch

From mrshirts at gmail.com  Thu Jan 16 05:23:39 2020
From: mrshirts at gmail.com (Michael Shirts)
Date: Thu, 16 Jan 2020 04:23:39 -0000
Subject: [gmx-users] Lambda Weights from Expanded Ensemble Code
In-Reply-To: <CAOKxWzJb8aUpQD5f6s_hAXp7cUOivRrO_BShJPxTWcuGnH9kQA@mail.gmail.com>
References: <CAOKxWzJb8aUpQD5f6s_hAXp7cUOivRrO_BShJPxTWcuGnH9kQA@mail.gmail.com>
Message-ID: <CA+zJb=j70oxwOFRqAVrnyHsk4rnW++b9ydibY_ggjY3ks53szg@mail.gmail.com>

The simulated tempering options haven't been as well tested as the
hamiltonian expanded ensemble version.  The weights SHOULD be showing up in
the column that says -nan, but clearly they aren't.  If you file a redmine
issue, I may be able to take a look, but it might take a while to address.

On Wed, Jan 15, 2020 at 8:52 PM Daniel Kozuch <dkozuch at princeton.edu> wrote:

> Hello,
>
> I am interested in using simulated tempering in GROMACS (2019.5) under the
> expanded ensemble options. Is there a way to monitor the ensemble weights
> as the simulation progresses? I think in theory they are supposed to be
> printed out in the log file, but it is only printing 0, -nan, and inf:
>
>             MC-lambda information
>   N  Temp.(K)    Count   G(in kT)  dG(in kT)
> ...
>  36  359.105      118       -nan       -nan <<
>  37  366.880       96       -nan       -nan
>  38  374.852      107       -nan       -nan
>  39  383.026      129       -nan       -nan
>  40  391.407      166       -nan       -nan
>  41  400.000      199       -nan    0.00000
>
> Here are my relevant mdp settings:
> simulated-tempering             = yes
> nstexpanded                     = 500
> simulated-tempering-scaling     = exponential
> lmc-stats                       = metropolis-transition
> lmc-move                        = metropolis
>
> Any suggestions?
>
> Best,
> Dan Kozuch
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From shlomit.afgin at weizmann.ac.il  Thu Jan 16 07:27:14 2020
From: shlomit.afgin at weizmann.ac.il (Shlomit Afgin)
Date: Thu, 16 Jan 2020 06:27:14 -0000
Subject: [gmx-users] Error:  Cannot find AVX 512F compiler flag
In-Reply-To: <20200115100652.GO7760@sillage.bis.pasteur.fr>
References: <CBF906C1-9C73-46E7-8D4A-9FC14F8030CF@weizmann.ac.il>
	<20200115100652.GO7760@sillage.bis.pasteur.fr>
Message-ID: <A6371EA0-BD46-49FE-A439-89042813B421@weizmann.ac.il>



How can I make GROMACS use devtoolset-6?





[shlomit at cn gromacs-2019.5]$ type gcc

gcc is /bin/gcc

[shlomit at cn gromacs-2019.5]$ scl enable devtoolset-6 bash

[shlomit at cn gromacs-2019.5]$ type gcc

gcc is /bin/gcc



Shlomit





?On 15/01/2020, 12:07, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Tru Huynh" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of tru at pasteur.fr> wrote:



    On Wed, Jan 15, 2020 at 08:50:46AM +0000, Shlomit Afgin wrote:

    >

    > Hi,

    > I tried to install GROMACS 2019.5 on CentOS7,

    > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON

    >

    > I have already installed devtoolset-6 and still get this error:

    installed, but not using it?



    [tru at elitebook840g3 ~]$ type gcc

    gcc is /usr/bin/gcc

    [tru at elitebook840g3 ~]$ scl enable devtoolset-6 bash

    [tru at elitebook840g3 ~]$ type gcc

    gcc is /opt/rh/devtoolset-6/root/usr/bin/gcc



    Tru



    --

    Tru Huynh (PhD) | mailto:tru at pasteur.fr | tel +33 1 45 68 87 37

    https://research.pasteur.fr/en/team/structural-bioinformatics/

    Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France

    --

    Gromacs Users mailing list



    * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!



    * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists



    * For (un)subscribe requests visit

    https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.



From blau at kth.se  Thu Jan 16 10:04:06 2020
From: blau at kth.se (Christian Blau)
Date: Thu, 16 Jan 2020 09:04:06 -0000
Subject: [gmx-users] gmx genconf
In-Reply-To: <CAEDv6u5V6_4vtyAiNBQpyxWZaFUB5Un_qjFg1HaqEHa7QTejWg@mail.gmail.com>
References: <CAEDv6u5V6_4vtyAiNBQpyxWZaFUB5Un_qjFg1HaqEHa7QTejWg@mail.gmail.com>
Message-ID: <1c7ba71e-8c83-8701-0788-95f7bf8c37f2@kth.se>

Hi Alex,


It's not possible with genconf. genconf only ever outputs a single 
structure. If you provide a trajectory, each frame in the trajectory is 
matched with a grid position that is then output as a single structure.

If you're looking into this for the sake of visualisation, tools like 
vmd and pymol usually do provide the functionality to generate periodic 
images. If you're after some analysis, it's often better to make use of 
the symmetry properties in the analysis explicitly rather than doubling 
the data.


Best,

Christian

On 2020-01-15 19:10, Alex wrote:
> Dear all,
> I am aware of the "gmx genconf -f time.gro -nbox 2 2 2 -o 2times.gro" in
> order to expand a gro file 2 times in all directions. I wonder if it is
> possible to expand a xtc trajectory and outpout a larger trajectory in the
> same way?
>
> According to genconf man page I see that the input could be -trj.xtc, but
> no trajectory as output has been mentioned there apparently.
>
> Regards,
> Alex

From alessandra.villa.biosim at gmail.com  Thu Jan 16 10:08:32 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Thu, 16 Jan 2020 09:08:32 -0000
Subject: [gmx-users] gmx genconf
In-Reply-To: <CAEDv6u5V6_4vtyAiNBQpyxWZaFUB5Un_qjFg1HaqEHa7QTejWg@mail.gmail.com>
References: <CAEDv6u5V6_4vtyAiNBQpyxWZaFUB5Un_qjFg1HaqEHa7QTejWg@mail.gmail.com>
Message-ID: <CANogp5w5z_1ZFvEfit0ChHaVvfkbTAVmDt4+p9dj0t7m8vyupg@mail.gmail.com>

Hi,

gmx genconf is not generating xtc files.  -trj  option allows to use the
trj frames to expand  gro/pdb files.
For example using   -nbox 2 2 2 the first 8 frames of the trj file will be
use to build the new gro/pdb file.

A possible alternative is to use If you want to visualize you xtc-file
extanded in x, y, z direction, you could use VMD.
Go to  graphics > representation >  periodic
and then select the directions and the n of images that you desire.

Best regards
Alessandra



On Wed, Jan 15, 2020 at 7:11 PM Alex <alexanderwien2k at gmail.com> wrote:

> Dear all,
> I am aware of the "gmx genconf -f time.gro -nbox 2 2 2 -o 2times.gro" in
> order to expand a gro file 2 times in all directions. I wonder if it is
> possible to expand a xtc trajectory and outpout a larger trajectory in the
> same way?
>
> According to genconf man page I see that the input could be -trj.xtc, but
> no trajectory as output has been mentioned there apparently.
>
> Regards,
> Alex
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Thu Jan 16 10:08:33 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Thu, 16 Jan 2020 09:08:33 -0000
Subject: [gmx-users] gmx genconf
In-Reply-To: <CAEDv6u5V6_4vtyAiNBQpyxWZaFUB5Un_qjFg1HaqEHa7QTejWg@mail.gmail.com>
References: <CAEDv6u5V6_4vtyAiNBQpyxWZaFUB5Un_qjFg1HaqEHa7QTejWg@mail.gmail.com>
Message-ID: <CANogp5w5z_1ZFvEfit0ChHaVvfkbTAVmDt4+p9dj0t7m8vyupg@mail.gmail.com>

Hi,

gmx genconf is not generating xtc files.  -trj  option allows to use the
trj frames to expand  gro/pdb files.
For example using   -nbox 2 2 2 the first 8 frames of the trj file will be
use to build the new gro/pdb file.

A possible alternative is to use If you want to visualize you xtc-file
extanded in x, y, z direction, you could use VMD.
Go to  graphics > representation >  periodic
and then select the directions and the n of images that you desire.

Best regards
Alessandra



On Wed, Jan 15, 2020 at 7:11 PM Alex <alexanderwien2k at gmail.com> wrote:

> Dear all,
> I am aware of the "gmx genconf -f time.gro -nbox 2 2 2 -o 2times.gro" in
> order to expand a gro file 2 times in all directions. I wonder if it is
> possible to expand a xtc trajectory and outpout a larger trajectory in the
> same way?
>
> According to genconf man page I see that the input could be -trj.xtc, but
> no trajectory as output has been mentioned there apparently.
>
> Regards,
> Alex
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Thu Jan 16 10:20:59 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Thu, 16 Jan 2020 09:20:59 -0000
Subject: [gmx-users] cut-off scheme
In-Reply-To: <CACrPy4B7niyieTA7X_vPVap5VdMS5Ed1p5JRvr47spb=ZmOFmA@mail.gmail.com>
References: <CACrPy4B7niyieTA7X_vPVap5VdMS5Ed1p5JRvr47spb=ZmOFmA@mail.gmail.com>
Message-ID: <CANogp5wo8vFv5hzhf9EV2BaRSXeQ0HcwVGT3NXOHtdih0nkH1A@mail.gmail.com>

Hi,

my suggestion is to move to Verlet scheme -
(http://manual.gromacs.org/documentation/2019/user-guide/cutoff-schemes.html
)
See also for
http://manual.gromacs.org/documentation/2020/release-notes/2019/major/deprecated-functionality.html#functionality-deprecated-in-gromacs-2019

You could compare the results coming from two schemes using the same
GROMACS version, paying particular attention to the properties of your
interest, and on the properties on which the parameterization is based on
(if possible). The results should be very similar.
Best regards
Alessandra




On Tue, Jan 14, 2020 at 8:29 PM Dhrubajyoti Maji <dmaji43 at gmail.com> wrote:

> Dear all,
>          I have found in some old literatures where force field
> parmetrizations were done, they have used group cut-off scheme which was
> default in gromacs version then. Now, if I want to use those parameters in
> updated gromacs version, do I have to take cutoff scheme as group ? Or can
> I use Verlet as it is default now? Any kind of help will be appreciated.
> Thanks and regards,
> Dhrubajyoti Maji
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Thu Jan 16 10:21:00 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Thu, 16 Jan 2020 09:21:00 -0000
Subject: [gmx-users] cut-off scheme
In-Reply-To: <CACrPy4B7niyieTA7X_vPVap5VdMS5Ed1p5JRvr47spb=ZmOFmA@mail.gmail.com>
References: <CACrPy4B7niyieTA7X_vPVap5VdMS5Ed1p5JRvr47spb=ZmOFmA@mail.gmail.com>
Message-ID: <CANogp5wo8vFv5hzhf9EV2BaRSXeQ0HcwVGT3NXOHtdih0nkH1A@mail.gmail.com>

Hi,

my suggestion is to move to Verlet scheme -
(http://manual.gromacs.org/documentation/2019/user-guide/cutoff-schemes.html
)
See also for
http://manual.gromacs.org/documentation/2020/release-notes/2019/major/deprecated-functionality.html#functionality-deprecated-in-gromacs-2019

You could compare the results coming from two schemes using the same
GROMACS version, paying particular attention to the properties of your
interest, and on the properties on which the parameterization is based on
(if possible). The results should be very similar.
Best regards
Alessandra




On Tue, Jan 14, 2020 at 8:29 PM Dhrubajyoti Maji <dmaji43 at gmail.com> wrote:

> Dear all,
>          I have found in some old literatures where force field
> parmetrizations were done, they have used group cut-off scheme which was
> default in gromacs version then. Now, if I want to use those parameters in
> updated gromacs version, do I have to take cutoff scheme as group ? Or can
> I use Verlet as it is default now? Any kind of help will be appreciated.
> Thanks and regards,
> Dhrubajyoti Maji
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From mark.j.abraham at gmail.com  Thu Jan 16 10:21:54 2020
From: mark.j.abraham at gmail.com (Mark Abraham)
Date: Thu, 16 Jan 2020 09:21:54 -0000
Subject: [gmx-users] Error: Cannot find AVX 512F compiler flag
In-Reply-To: <8806AC21-F166-46FF-9926-6F44C5CDA7BD@weizmann.ac.il>
References: <CBF906C1-9C73-46E7-8D4A-9FC14F8030CF@weizmann.ac.il>
	<CANnYEw55zb9uD8j4T7fhhJLh0rNXECZscD30whSpKZNY6H+S4g@mail.gmail.com>
	<8806AC21-F166-46FF-9926-6F44C5CDA7BD@weizmann.ac.il>
Message-ID: <CAMNuMATtqS79VKWEtm_rCoix2e4SxWvCOT=16ZXT-_f-3O=duA@mail.gmail.com>

That tells you what your CPU is capable of. We need to know whether cmake
has found the compiler that can issue the instructions. Follow the
suggestions Roland and I have made.

Mark

On Wed, 15 Jan 2020 at 10:45, Shlomit Afgin <shlomit.afgin at weizmann.ac.il>
wrote:

>
>
> I ran:
>
> cat /proc/cpuinfo | grep -i avx512
>
>
>
> and got:
>
> avx512f avx512dq avx512cd avx512bw avx512vl
>
>
>
> So I thought I can use it. Am I wrong?
>
>
>
> Shlomit
>
>
>
> ?On 15/01/2020, 11:14, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> on behalf of Szil?rd P?ll" <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
> pall.szilard at gmail.com> wrote:
>
>
>
>     Hi,
>
>
>
>     What hardware are you targeting? Unless you need AVX512 support, you
> could
>
>     just manually specify the appropriate setting in GMX_SIMD, e.g.
>
>     -DGMX_SIMD=AVX2_256 would be appropriate for most cases where AVX512
> is not
>
>     supported.
>
>
>
>     Cheers,
>
>     --
>
>     Szil?rd
>
>
>
>
>
>     On Wed, Jan 15, 2020 at 9:51 AM Shlomit Afgin <
> shlomit.afgin at weizmann.ac.il>
>
>     wrote:
>
>
>
>     >
>
>     > Hi,
>
>     > I tried to install GROMACS 2019.5 on CentOS7,
>
>     > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
>
>     >
>
>     > I have already installed devtoolset-6 and still get this error:
>
>     >
>
>     > -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS
>
>     > -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Failed
>
>     > -- Could not find any flag to build test source (this could be due to
>
>     > either the compiler or binutils)
>
>     > -- Could not identify number of AVX-512 units - detection program
> missing
>
>     > compilation prerequisites
>
>     > -- Could not run code to detect number of AVX-512 FMA units -
> assuming 2.
>
>     > -- Detected best SIMD instructions for this CPU - AVX_512
>
>     > CMake Error at cmake/gmxManageSimd.cmake:51 (message):
>
>     >   Cannot find AVX 512F compiler flag.  Use a newer compiler, or
> choose a
>
>     >   lower level of SIMD (slower).
>
>     > Call Stack (most recent call first):
>
>     >   cmake/gmxManageSimd.cmake:186
>
>     > (gmx_give_fatal_error_when_simd_support_not_found)
>
>     >   CMakeLists.txt:719 (gmx_manage_simd)
>
>     >
>
>     >
>
>     > Thanks,
>
>     > Shlomit
>
>     > --
>
>     > Gromacs Users mailing list
>
>     >
>
>     > * Please search the archive at
>
>     > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>
>     > posting!
>
>     >
>
>     > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>     >
>
>     > * For (un)subscribe requests visit
>
>     > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
>
>     > send a mail to gmx-users-request at gromacs.org.
>
>     >
>
>     --
>
>     Gromacs Users mailing list
>
>
>
>     * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
>
>
>     * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>     * For (un)subscribe requests visit
>
>     https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

From alessandra.villa.biosim at gmail.com  Thu Jan 16 10:31:37 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Thu, 16 Jan 2020 09:31:37 -0000
Subject: [gmx-users] Regarding high RMSD
In-Reply-To: <CAG89CR5WTg2cd7H-JQuOsGmQ4WeEhLdM6V2Ux+1eA+YEm7KEgQ@mail.gmail.com>
References: <CAG89CR5WTg2cd7H-JQuOsGmQ4WeEhLdM6V2Ux+1eA+YEm7KEgQ@mail.gmail.com>
Message-ID: <CANogp5wyJ47oLMK-AJEoT5O2Y1eagUza5b+wiKgnuTgFgzRQyQ@mail.gmail.com>

Hi,
I suggest to visualize your trajectory. Maybe one of the peptide is
diffusing away from the other.
Or the one peptide is jumping in and out or moving out the box.
If it is the case, here you found some trjconv workflow
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Best regards
Alessandra


On Wed, Jan 15, 2020 at 11:21 AM Ashma Khan <ashmakhan200 at gmail.com> wrote:

> Dear all,
> I have calculated the c-alpha RMSD of dimer having 7 residues peptide each
> by using command gmx rms. But the calculated RMSD 14 Angstorm is very high,
> although I have applied all pbc conditions. Anybody can suggest me why so
> much high RMSD is coming or is it possible.
>
> --
> Ashma Khan
> Research Scholar
> Department of Chemistry
> AMU, Aligarh
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Thu Jan 16 10:31:41 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Thu, 16 Jan 2020 09:31:41 -0000
Subject: [gmx-users] Regarding high RMSD
In-Reply-To: <CAG89CR5WTg2cd7H-JQuOsGmQ4WeEhLdM6V2Ux+1eA+YEm7KEgQ@mail.gmail.com>
References: <CAG89CR5WTg2cd7H-JQuOsGmQ4WeEhLdM6V2Ux+1eA+YEm7KEgQ@mail.gmail.com>
Message-ID: <CANogp5wyJ47oLMK-AJEoT5O2Y1eagUza5b+wiKgnuTgFgzRQyQ@mail.gmail.com>

Hi,
I suggest to visualize your trajectory. Maybe one of the peptide is
diffusing away from the other.
Or the one peptide is jumping in and out or moving out the box.
If it is the case, here you found some trjconv workflow
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Best regards
Alessandra


On Wed, Jan 15, 2020 at 11:21 AM Ashma Khan <ashmakhan200 at gmail.com> wrote:

> Dear all,
> I have calculated the c-alpha RMSD of dimer having 7 residues peptide each
> by using command gmx rms. But the calculated RMSD 14 Angstorm is very high,
> although I have applied all pbc conditions. Anybody can suggest me why so
> much high RMSD is coming or is it possible.
>
> --
> Ashma Khan
> Research Scholar
> Department of Chemistry
> AMU, Aligarh
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Thu Jan 16 10:55:50 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Thu, 16 Jan 2020 09:55:50 -0000
Subject: [gmx-users] Troubleshooting Error Message: Invalid Index Group
	References
In-Reply-To: <BN8PR14MB317166F8297AB07F3187B89693340@BN8PR14MB3171.namprd14.prod.outlook.com>
References: <BN8PR14MB317166F8297AB07F3187B89693340@BN8PR14MB3171.namprd14.prod.outlook.com>
Message-ID: <CANogp5wCUbrJ7w_xxt9hWx41pQ3S-bhJTjOunC_Uh69On5rumg@mail.gmail.com>

Hi,

On Tue, Jan 14, 2020 at 7:41 PM Travis Meyer <travis.meyer at rutgers.edu>
wrote:

> Hello all,
>
> I am a brand new MD/GROMACS user, and I have been trying to learn how to
> use GROMACS for coarse-grained simulations using the MARTINI forcefield. I
> was going through a tutorial on coarse-graining from the MARTINI website (
> http://cgmartini.nl/index.php/tutorials-general-introduction-gmx5/martini-tutorials-polymers-gmx5)
> but ran into an error I have been not been able to find a solution for.
>
> After coarse-graining the all-atom simulation to the COM between 3 atoms,
> I need to calculate bond lengths and angles in order to parameterize bonded
> interactions. Following instructions from the tutorial, I created index
> files for all bonds, angles, and dihedrals and used gmx distance along with
> the coarse-grained trajectory file. After choosing which index group I want
> to use, I receive an error message:
>
> I am not familiar with the MARTINI tutorial, but I guess that the
particles numbers in your traj_cg are different from the one of
traj_allatoms.
Thus my suggestion is to check that the numbers reported in the index file
corresponds to the particles number that you have in your traj_cg.
The easy way to do it is to look  at  CG_gro file ( you can generate using
gmx traj in the same way that you have used for traj_cg

Best regards
Alessandra



> Inconsistency in user input: Invalid index group references encountered
> Group 'bonds_core1' cannot be used in selections, because it contains
> negative atom indices and/or references atoms not present (largest allowed
> atom index is 0).
>
> The index file itself contains all the proper atom indices. The fact that
> the error says "largest allowed atom index is 0" makes me think there is an
> error with my .xtc file, but I did not receive any errors when calculating
> angle distributions using the exact same trajectory file and appropriate
> angle index files.
>
> Are there any recommendations for how to go about fixing this?
>
> Thanks!
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Thu Jan 16 10:55:51 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Thu, 16 Jan 2020 09:55:51 -0000
Subject: [gmx-users] Troubleshooting Error Message: Invalid Index Group
	References
In-Reply-To: <BN8PR14MB317166F8297AB07F3187B89693340@BN8PR14MB3171.namprd14.prod.outlook.com>
References: <BN8PR14MB317166F8297AB07F3187B89693340@BN8PR14MB3171.namprd14.prod.outlook.com>
Message-ID: <CANogp5wCUbrJ7w_xxt9hWx41pQ3S-bhJTjOunC_Uh69On5rumg@mail.gmail.com>

Hi,

On Tue, Jan 14, 2020 at 7:41 PM Travis Meyer <travis.meyer at rutgers.edu>
wrote:

> Hello all,
>
> I am a brand new MD/GROMACS user, and I have been trying to learn how to
> use GROMACS for coarse-grained simulations using the MARTINI forcefield. I
> was going through a tutorial on coarse-graining from the MARTINI website (
> http://cgmartini.nl/index.php/tutorials-general-introduction-gmx5/martini-tutorials-polymers-gmx5)
> but ran into an error I have been not been able to find a solution for.
>
> After coarse-graining the all-atom simulation to the COM between 3 atoms,
> I need to calculate bond lengths and angles in order to parameterize bonded
> interactions. Following instructions from the tutorial, I created index
> files for all bonds, angles, and dihedrals and used gmx distance along with
> the coarse-grained trajectory file. After choosing which index group I want
> to use, I receive an error message:
>
> I am not familiar with the MARTINI tutorial, but I guess that the
particles numbers in your traj_cg are different from the one of
traj_allatoms.
Thus my suggestion is to check that the numbers reported in the index file
corresponds to the particles number that you have in your traj_cg.
The easy way to do it is to look  at  CG_gro file ( you can generate using
gmx traj in the same way that you have used for traj_cg

Best regards
Alessandra



> Inconsistency in user input: Invalid index group references encountered
> Group 'bonds_core1' cannot be used in selections, because it contains
> negative atom indices and/or references atoms not present (largest allowed
> atom index is 0).
>
> The index file itself contains all the proper atom indices. The fact that
> the error says "largest allowed atom index is 0" makes me think there is an
> error with my .xtc file, but I did not receive any errors when calculating
> angle distributions using the exact same trajectory file and appropriate
> angle index files.
>
> Are there any recommendations for how to go about fixing this?
>
> Thanks!
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Thu Jan 16 11:17:36 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Thu, 16 Jan 2020 10:17:36 -0000
Subject: [gmx-users] com motion and position restraints may cause
	artifacts
In-Reply-To: <CAAHQ3wkvyk9UmO_5=YYEVQLhtetEEVwqVXp-jyEY55DgW-sRqg@mail.gmail.com>
References: <CAAHQ3wkvyk9UmO_5=YYEVQLhtetEEVwqVXp-jyEY55DgW-sRqg@mail.gmail.com>
Message-ID: <CANogp5wm2T7QDHG5wpw16PBqqXvBU=YKUckdAT5a4-k-+JMmyQ@mail.gmail.com>

Hi,

On Mon, Jan 13, 2020 at 3:36 PM Christos Deligkaris <deligkaris at gmail.com>
wrote:

> dear all,
>
> I installed gromacs 2020 and I now get the following message during
> equilibration:
>
> NOTE 1 [file nvt.mdp]:
>
>   Removing center of mass motion in the presence of position
> restraints  might cause artifacts
>
> I do not recall seeing this with gromacs 2018. In which cases are
> artifacts created? Is it now recommended to not remove the center of
> mass motion during equilibration?
>
>
It is recommended not to have position restrain and remove of center of
mass at the same moment. That is also the case of the equilibration phase.
That may cause artifact depending on the system and the condition you are
simulating.

Best regards
Alessandra




> Best wishes,
>
> Christos Deligkaris, PhD
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Thu Jan 16 11:17:36 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Thu, 16 Jan 2020 10:17:36 -0000
Subject: [gmx-users] com motion and position restraints may cause
	artifacts
In-Reply-To: <CAAHQ3wkvyk9UmO_5=YYEVQLhtetEEVwqVXp-jyEY55DgW-sRqg@mail.gmail.com>
References: <CAAHQ3wkvyk9UmO_5=YYEVQLhtetEEVwqVXp-jyEY55DgW-sRqg@mail.gmail.com>
Message-ID: <CANogp5wm2T7QDHG5wpw16PBqqXvBU=YKUckdAT5a4-k-+JMmyQ@mail.gmail.com>

Hi,

On Mon, Jan 13, 2020 at 3:36 PM Christos Deligkaris <deligkaris at gmail.com>
wrote:

> dear all,
>
> I installed gromacs 2020 and I now get the following message during
> equilibration:
>
> NOTE 1 [file nvt.mdp]:
>
>   Removing center of mass motion in the presence of position
> restraints  might cause artifacts
>
> I do not recall seeing this with gromacs 2018. In which cases are
> artifacts created? Is it now recommended to not remove the center of
> mass motion during equilibration?
>
>
It is recommended not to have position restrain and remove of center of
mass at the same moment. That is also the case of the equilibration phase.
That may cause artifact depending on the system and the condition you are
simulating.

Best regards
Alessandra




> Best wishes,
>
> Christos Deligkaris, PhD
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Thu Jan 16 11:20:33 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Thu, 16 Jan 2020 10:20:33 -0000
Subject: [gmx-users] A list of missing interactions
In-Reply-To: <CAH9Uu9PfmNEdMs1gx7iQ0Oz6R98z+guMNDqMsHz2VD0k6YpRLw@mail.gmail.com>
References: <CAH9Uu9PfmNEdMs1gx7iQ0Oz6R98z+guMNDqMsHz2VD0k6YpRLw@mail.gmail.com>
Message-ID: <CANogp5yRk7uL=t+FQk05sVH7FPAzHcs1xG-4oxYzWSo512RZJg@mail.gmail.com>

Hi,
my suggestion is to follow the indication that you got from the error
See the mdrun " option -rdd, for pairs and tabulated bonds also see option
-ddcheck"
Best regards
Alessandra



On Wed, Jan 15, 2020 at 12:33 AM Sadaf Rani <sadafrani6 at gmail.com> wrote:

> Dear Gromacs users
> I am facing this error during free energy calculation of protein-ligand for
> which I have applied restrained to some atoms of protein residue and
> ligand.
> A list of missing interactions:
>       Restraint Pot. of      1 missing      1
>
> Molecule type 'Protein'
> the first 10 missing interactions, except for exclusions:
>       Restraint Pot. atoms 3437 7908           global  3437  7908
>
> -------------------------------------------------------
> Program:     gmx mdrun, version 2018.1
> Source file: src/gromacs/domdec/domdec_topology.cpp (line 436)
> MPI rank:    0 (out of 2)
>
> Fatal error:
> 1 of the 64584 bonded interactions could not be calculated because some
> atoms
> involved moved further apart than the multi-body cut-off distance (4.47682
> nm)
> or the two-body cut-off distance (4.47682 nm), see option -rdd, for pairs
> and
> tabulated bonds also see option -ddcheck
>
> Could anybody please suggest how should I fix this error? I would be really
> thankful.
>
> Regards
>
> Sadaf
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Thu Jan 16 11:20:33 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Thu, 16 Jan 2020 10:20:33 -0000
Subject: [gmx-users] A list of missing interactions
In-Reply-To: <CAH9Uu9PfmNEdMs1gx7iQ0Oz6R98z+guMNDqMsHz2VD0k6YpRLw@mail.gmail.com>
References: <CAH9Uu9PfmNEdMs1gx7iQ0Oz6R98z+guMNDqMsHz2VD0k6YpRLw@mail.gmail.com>
Message-ID: <CANogp5yRk7uL=t+FQk05sVH7FPAzHcs1xG-4oxYzWSo512RZJg@mail.gmail.com>

Hi,
my suggestion is to follow the indication that you got from the error
See the mdrun " option -rdd, for pairs and tabulated bonds also see option
-ddcheck"
Best regards
Alessandra



On Wed, Jan 15, 2020 at 12:33 AM Sadaf Rani <sadafrani6 at gmail.com> wrote:

> Dear Gromacs users
> I am facing this error during free energy calculation of protein-ligand for
> which I have applied restrained to some atoms of protein residue and
> ligand.
> A list of missing interactions:
>       Restraint Pot. of      1 missing      1
>
> Molecule type 'Protein'
> the first 10 missing interactions, except for exclusions:
>       Restraint Pot. atoms 3437 7908           global  3437  7908
>
> -------------------------------------------------------
> Program:     gmx mdrun, version 2018.1
> Source file: src/gromacs/domdec/domdec_topology.cpp (line 436)
> MPI rank:    0 (out of 2)
>
> Fatal error:
> 1 of the 64584 bonded interactions could not be calculated because some
> atoms
> involved moved further apart than the multi-body cut-off distance (4.47682
> nm)
> or the two-body cut-off distance (4.47682 nm), see option -rdd, for pairs
> and
> tabulated bonds also see option -ddcheck
>
> Could anybody please suggest how should I fix this error? I would be really
> thankful.
>
> Regards
>
> Sadaf
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From dmaji43 at gmail.com  Thu Jan 16 11:43:33 2020
From: dmaji43 at gmail.com (Dhrubajyoti Maji)
Date: Thu, 16 Jan 2020 10:43:33 -0000
Subject: [gmx-users] cut-off scheme
In-Reply-To: <CANogp5wo8vFv5hzhf9EV2BaRSXeQ0HcwVGT3NXOHtdih0nkH1A@mail.gmail.com>
References: <CACrPy4B7niyieTA7X_vPVap5VdMS5Ed1p5JRvr47spb=ZmOFmA@mail.gmail.com>
	<CANogp5wo8vFv5hzhf9EV2BaRSXeQ0HcwVGT3NXOHtdih0nkH1A@mail.gmail.com>
Message-ID: <CACrPy4AtAB_EPi+5nr9c4fiPycgzm6_WTkF847sJbLz6XPyr0A@mail.gmail.com>

Many thanks for your reply. These links are really helpful.

On Thu, 16 Jan 2020 at 14:51, Alessandra Villa <
alessandra.villa.biosim at gmail.com> wrote:

> Hi,
>
> my suggestion is to move to Verlet scheme -
> (
> http://manual.gromacs.org/documentation/2019/user-guide/cutoff-schemes.html
> )
> See also for
>
> http://manual.gromacs.org/documentation/2020/release-notes/2019/major/deprecated-functionality.html#functionality-deprecated-in-gromacs-2019
>
> You could compare the results coming from two schemes using the same
> GROMACS version, paying particular attention to the properties of your
> interest, and on the properties on which the parameterization is based on
> (if possible). The results should be very similar.
> Best regards
> Alessandra
>
>
>
>
> On Tue, Jan 14, 2020 at 8:29 PM Dhrubajyoti Maji <dmaji43 at gmail.com>
> wrote:
>
> > Dear all,
> >          I have found in some old literatures where force field
> > parmetrizations were done, they have used group cut-off scheme which was
> > default in gromacs version then. Now, if I want to use those parameters
> in
> > updated gromacs version, do I have to take cutoff scheme as group ? Or
> can
> > I use Verlet as it is default now? Any kind of help will be appreciated.
> > Thanks and regards,
> > Dhrubajyoti Maji
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From dmaji43 at gmail.com  Thu Jan 16 11:43:33 2020
From: dmaji43 at gmail.com (Dhrubajyoti Maji)
Date: Thu, 16 Jan 2020 10:43:33 -0000
Subject: [gmx-users] cut-off scheme
In-Reply-To: <CANogp5wo8vFv5hzhf9EV2BaRSXeQ0HcwVGT3NXOHtdih0nkH1A@mail.gmail.com>
References: <CACrPy4B7niyieTA7X_vPVap5VdMS5Ed1p5JRvr47spb=ZmOFmA@mail.gmail.com>
	<CANogp5wo8vFv5hzhf9EV2BaRSXeQ0HcwVGT3NXOHtdih0nkH1A@mail.gmail.com>
Message-ID: <CACrPy4AtAB_EPi+5nr9c4fiPycgzm6_WTkF847sJbLz6XPyr0A@mail.gmail.com>

Many thanks for your reply. These links are really helpful.

On Thu, 16 Jan 2020 at 14:51, Alessandra Villa <
alessandra.villa.biosim at gmail.com> wrote:

> Hi,
>
> my suggestion is to move to Verlet scheme -
> (
> http://manual.gromacs.org/documentation/2019/user-guide/cutoff-schemes.html
> )
> See also for
>
> http://manual.gromacs.org/documentation/2020/release-notes/2019/major/deprecated-functionality.html#functionality-deprecated-in-gromacs-2019
>
> You could compare the results coming from two schemes using the same
> GROMACS version, paying particular attention to the properties of your
> interest, and on the properties on which the parameterization is based on
> (if possible). The results should be very similar.
> Best regards
> Alessandra
>
>
>
>
> On Tue, Jan 14, 2020 at 8:29 PM Dhrubajyoti Maji <dmaji43 at gmail.com>
> wrote:
>
> > Dear all,
> >          I have found in some old literatures where force field
> > parmetrizations were done, they have used group cut-off scheme which was
> > default in gromacs version then. Now, if I want to use those parameters
> in
> > updated gromacs version, do I have to take cutoff scheme as group ? Or
> can
> > I use Verlet as it is default now? Any kind of help will be appreciated.
> > Thanks and regards,
> > Dhrubajyoti Maji
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From janbre at amu.edu.pl  Thu Jan 16 11:54:57 2020
From: janbre at amu.edu.pl (Jan Brezovsky)
Date: Thu, 16 Jan 2020 10:54:57 -0000
Subject: [gmx-users] Available Post-doc position
Message-ID: <c20f57f0-f016-5f31-f0ec-e06456e6e5a9@amu.edu.pl>

Dear colleagues,

we have an open Post-doc position for those interested in the 
biomolecular simulations, and in particular ligand-transport mechanisms 
in enzymatic action, and/or method developement. The position is available
asap, - for details please see: 
https://www.iimcb.gov.pl/en/new-jobs-positions/292-postdoc-position

Many thanks and sincere apology to those not interested.

Best regards,
Jan

-- 
______________________________________________________

Jan Brezovsky, Ph.D.
Prof. UAM & IIMCB, Head of Laboratory of Biomolecular
Interactions and Transport
______________________________________________________

Institute of Molecular Biology and Biotechnology
Faculty of Biology
Adam Mickiewicz University
Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland

and

International Institute of Molecular and Cell Biology
Trojdena 4, 02-109 Warsaw, Poland

phone: +48 61 829 5839
e-mails: janbre at amu.edu.pl, jbrezovsky at iimcb.gov.pl
http://labbit.eu
______________________________________________________


From jalemkul at vt.edu  Thu Jan 16 12:19:27 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Thu, 16 Jan 2020 11:19:27 -0000
Subject: [gmx-users] Hydrogen bonding criteria in Gromacs
In-Reply-To: <CAHXfRVNQ0Kg-8LqqtSFkx0kjYB=gB7x2o8v0N1q_KnSLkHCZ2Q@mail.gmail.com>
References: <DB6PR0101MB2424708E45DFBC1D054F3E52EB370@DB6PR0101MB2424.eurprd01.prod.exchangelabs.com>
	<e846b411-71ae-1a7a-2936-7ed5f757fdc7@vt.edu>
	<CAHXfRVNQ0Kg-8LqqtSFkx0kjYB=gB7x2o8v0N1q_KnSLkHCZ2Q@mail.gmail.com>
Message-ID: <eab5575d-29f2-b427-49dd-ffa8607465aa@vt.edu>



On 1/15/20 10:05 PM, Myunggi Yi wrote:
> Dear Dr. Justin Lemkul,
>
> Can you explain why the D-H-A is 150?
>
> If H-D-A is 30, then D-H-A should be smaller than 150 degrees.
> Since the sum of interior angles of a triangle should be 180 degrees...
> See the following triangle.
>
>                       H
>
> D                                                           A
>
>
> Am I missing something?
>

It's a deviation from linearity. An ideal hydrogen bond has a D-H-A 
angle of 180, thus H-D-A of 0. So the 30 degree values specified in 
GROMACS is effectively the deviation from linearity rather than being 
the complement of this value, which other software uses.

-Justin

> On Thu, Jan 16, 2020 at 2:30 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 1/15/20 11:57 AM, Pandya, Akash wrote:
>>> Hi all,
>>>
>>> I  wanted to ask a couple of questions about the hydrogen bonding
>> calculation in Gromacs.
>>>
>>>     1.   Why is the default angle cutoff 30 degrees? The reason I ask
>> this is because I?ve seen in other packages with higher angle cutoffs.
>>
>> It depends on how the software defines the angle. The GROMACS convention
>> is the angle corresponds to H-D-A rather than D-H-A like some other
>> programs. H-D-A cutoff of 30 degrees is equivalent to the "conventional"
>> 150-degree D-H-A cutoff.
>>
>>>     2.  What?s the best way to define cutoffs for my system? I know this
>> is ambiguous, but is there a procedure I can use to decide?
>>
>> The default criteria are widely used and usually don't require any tuning.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From jalemkul at vt.edu  Thu Jan 16 12:20:37 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Thu, 16 Jan 2020 11:20:37 -0000
Subject: [gmx-users] com motion and position restraints may cause
 artifacts
In-Reply-To: <CANogp5wm2T7QDHG5wpw16PBqqXvBU=YKUckdAT5a4-k-+JMmyQ@mail.gmail.com>
References: <CAAHQ3wkvyk9UmO_5=YYEVQLhtetEEVwqVXp-jyEY55DgW-sRqg@mail.gmail.com>
	<CANogp5wm2T7QDHG5wpw16PBqqXvBU=YKUckdAT5a4-k-+JMmyQ@mail.gmail.com>
Message-ID: <d2752133-25de-0e26-1266-4c5f599e0122@vt.edu>



On 1/16/20 5:17 AM, Alessandra Villa wrote:
> Hi,
>
> On Mon, Jan 13, 2020 at 3:36 PM Christos Deligkaris <deligkaris at gmail.com>
> wrote:
>
>> dear all,
>>
>> I installed gromacs 2020 and I now get the following message during
>> equilibration:
>>
>> NOTE 1 [file nvt.mdp]:
>>
>>    Removing center of mass motion in the presence of position
>> restraints  might cause artifacts
>>
>> I do not recall seeing this with gromacs 2018. In which cases are
>> artifacts created? Is it now recommended to not remove the center of
>> mass motion during equilibration?
>>
>>
> It is recommended not to have position restrain and remove of center of
> mass at the same moment. That is also the case of the equilibration phase.
> That may cause artifact depending on the system and the condition you are
> simulating.

What is the nature of these artifacts and where is this documented? 
Combining position restraints with COM motion removal is an extremely 
common practice. Phrases like "might cause artifacts" are troubling 
because that implies uncertainty. Are there cases when this combination 
does not cause artifacts?

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From wacha.andras at ttk.hu  Thu Jan 16 14:13:43 2020
From: wacha.andras at ttk.hu (=?UTF-8?Q?Andr=c3=a1s_Ferenc_WACHA?=)
Date: Thu, 16 Jan 2020 13:13:43 -0000
Subject: [gmx-users] pdb2gmx picks up the wrong .tdb files?
Message-ID: <bb2d0e87-595d-f6e5-d471-8c8e031168e7@ttk.hu>

Dear fellow Gromacs users,

I have developed an extended version of the CHARMM36m force field for
beta-amino acids (https://charmm-betaff.readthedocs.io,
https://gitlab.com/awacha/charmm-beta.ff). For beta-amino acids I found
pdb2gmx works well. However, if I try to use it for natural peptides and
proteins (e.g. 6LYZ from the PDB), the following command:

gmx pdb2gmx -f 6LYZ.pdb, -ff charmm-beta -ter -ignh

fails to recognize the correct termini database files. The output is the
following:

(-------------------------- START of gmx output
-----------------------------------)

GROMACS:????? gmx pdb2gmx, version 2020
Executable:??
/opt/spack/opt/spack/linux-archrolling-skylake/gcc-9.2.0/gromacs-2020-ls53yrft6droj2ovhuzdwdufi4an4vir/bin/gmx
Data prefix:?
/opt/spack/opt/spack/linux-archrolling-skylake/gcc-9.2.0/gromacs-2020-ls53yrft6droj2ovhuzdwdufi4an4vir
Working dir:? /home/wachaandras/gromacs/forcefields
Command line:
? gmx pdb2gmx -f 6lyz.pdb -ff charmm-beta -ter -ignh

Using the Charmm-beta force field in directory ./charmm-beta.ff

Opening force field file ./charmm-beta.ff/watermodels.dat

Select the Water Model:
?1: TIP3P??? TIP 3-point, recommended, by default uses CHARMM TIP3 with
LJ on H
?2: TIP4P??? TIP 4-point
?3: TIP5P??? TIP 5-point
?4: SPC??? ??? simple point charge
?5: SPC/E??? extended simple point charge
?6: Methanol?? Equilibrated methanol
?7: Octanol??? Equilibrated octanol
?8: None
1
going to rename ./charmm-beta.ff/merged.r2b
Opening force field file ./charmm-beta.ff/merged.r2b
Reading 6lyz.pdb...
WARNING: all CONECT records are ignored
Read '', 1001 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 129 residues with 1001 atoms

? chain? #res #atoms
? 1 'A'?? 129?? 1001?

All occupancies are one
Opening force field file ./charmm-beta.ff/atomtypes.atp
Opening force field file ./charmm-beta.ff/betaaminoacids.atp
Opening force field file ./charmm-beta.ff/cyclicbeta.atp
Reading residue database... (Charmm-beta)
Opening force field file ./charmm-beta.ff/betaaminoacids.rtp
Opening force field file ./charmm-beta.ff/cyclicbeta.rtp
Opening force field file ./charmm-beta.ff/extra.rtp
Warning: file does not end with a newline, last line:
;
Opening force field file ./charmm-beta.ff/merged.rtp
Opening force field file ./charmm-beta.ff/merged.hdb
Opening force field file ./charmm-beta.ff/betaaminoacids.n.tdb
Opening force field file ./charmm-beta.ff/cyclicbeta.n.tdb
Opening force field file ./charmm-beta.ff/merged.n.tdb
Opening force field file ./charmm-beta.ff/betaaminoacids.c.tdb
Opening force field file ./charmm-beta.ff/cyclicbeta.c.tdb
Opening force field file ./charmm-beta.ff/merged.c.tdb
Processing chain 1 'A' (1001 atoms, 129 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
?protonation. 213 donors and 184 acceptors were found.
There are 262 hydrogen bonds
Will use HISD for residue 15
Identified residue LYS1 as a starting terminus.
Identified residue LEU129 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
??????????????????? CYS6?? MET12?? HIS15?? CYS30?? CYS64?? CYS76?? CYS80
??????????????????? SG48??? SD87? NE2118?? SG238?? SG513?? SG601?? SG630
?? MET12??? SD87?? 1.205
?? HIS15? NE2118?? 1.804?? 0.998
?? CYS30?? SG238?? 1.450?? 1.070?? 2.063
?? CYS64?? SG513?? 2.873?? 1.779?? 1.755?? 2.236
?? CYS76?? SG601?? 2.740?? 1.544?? 1.418?? 2.132?? 0.778
?? CYS80?? SG630?? 3.006?? 1.943?? 1.892?? 2.387?? 0.200?? 0.958
?? CYS94?? SG724?? 2.576?? 1.388?? 1.329?? 1.976?? 0.678?? 0.211?? 0.871
? MET105?? SD799?? 1.866?? 0.933?? 1.679?? 0.896?? 1.858?? 1.483?? 2.047
? CYS115?? SG889?? 1.625?? 1.099?? 2.068?? 0.204?? 2.108?? 2.005?? 2.260
? CYS127?? SG981?? 0.203?? 1.089?? 1.733?? 1.332?? 2.808?? 2.631?? 2.950
?????????????????? CYS94? MET105? CYS115
?????????????????? SG724?? SD799?? SG889
? MET105?? SD799?? 1.389
? CYS115?? SG889?? 1.855?? 0.790
? CYS127?? SG981?? 2.474?? 1.701?? 1.505
Linking CYS-6 SG-48 and CYS-127 SG-981...
Linking CYS-30 SG-238 and CYS-115 SG-889...
Linking CYS-64 SG-513 and CYS-80 SG-630...
Linking CYS-76 SG-601 and CYS-94 SG-724...
Select start terminus type for LYS-1
?0: Beta3NH3+
?1: Beta2NH3+
?2: Beta23NH3+
?3: B3_NH2
?4: B2_NH2
?5: B23_NH2
?6: 5TER
?7: None

(-------------------------- END of gmx output
-----------------------------------)

Information in the force field relevant to the beta-peptides is stored
in betaaminoacids.{arn,atp,c.tdb,n.tdb,rtp} files. I have kept the
original ones (merged.*) intact. From the output above it seems that
pdb2gmx recognizes and loads all the relevant files (both
betaaminoacids.* and merged.*), but only shows a selection of N-terminal
patches from the betaaminoacids.n.tdb file. More precisely, the 5TER
terminus is from merged.n.tdb, but the other ones before it get
overridden by entries from betaaminoacids.n.tdb. Is there some rule in
pdb2gmx which considers some endgroups equivalent and keeps only one? I
have encountered it neither in the main documentation (section 5.6.5:
pdb2gmx input files), nor in the help of gmx pdb2gmx.

Could anyone point me to how I should do this correctly?

Kind regards,

Andras

-- 
Andr?s Ferenc Wacha, PhD
research fellow, CREDO instrument responsible

Biological Nanochemistry Research Group (310)

Institute of Materials and Environmental Chemistry
Research Centre for Natural Sciences (RCNS)
Magyar tud?sok k?r?tja 2.
H-1117 Budapest, Hungary
Phone: +36-1-382-6427
Web: http://bionano.ttk.hu
CREDO SAXS instrument: http://credo.ttk.hu

-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 554 bytes
Desc: OpenPGP digital signature
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20200116/1df6b230/attachment-0001.sig>

From jalemkul at vt.edu  Thu Jan 16 14:34:09 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Thu, 16 Jan 2020 13:34:09 -0000
Subject: [gmx-users] pdb2gmx picks up the wrong .tdb files?
In-Reply-To: <bb2d0e87-595d-f6e5-d471-8c8e031168e7@ttk.hu>
References: <bb2d0e87-595d-f6e5-d471-8c8e031168e7@ttk.hu>
Message-ID: <3fa389b9-ec22-aa09-d112-05cdef3e09aa@vt.edu>



On 1/16/20 8:04 AM, Andr?s Ferenc WACHA wrote:
> Dear fellow Gromacs users,
>
> I have developed an extended version of the CHARMM36m force field for
> beta-amino acids (https://charmm-betaff.readthedocs.io,
> https://gitlab.com/awacha/charmm-beta.ff). For beta-amino acids I found
> pdb2gmx works well. However, if I try to use it for natural peptides and
> proteins (e.g. 6LYZ from the PDB), the following command:
>
> gmx pdb2gmx -f 6LYZ.pdb, -ff charmm-beta -ter -ignh
>
> fails to recognize the correct termini database files. The output is the
> following:
>
> (-------------------------- START of gmx output
> -----------------------------------)
>
> GROMACS:????? gmx pdb2gmx, version 2020
> Executable:
> /opt/spack/opt/spack/linux-archrolling-skylake/gcc-9.2.0/gromacs-2020-ls53yrft6droj2ovhuzdwdufi4an4vir/bin/gmx
> Data prefix:
> /opt/spack/opt/spack/linux-archrolling-skylake/gcc-9.2.0/gromacs-2020-ls53yrft6droj2ovhuzdwdufi4an4vir
> Working dir:? /home/wachaandras/gromacs/forcefields
> Command line:
>  ? gmx pdb2gmx -f 6lyz.pdb -ff charmm-beta -ter -ignh
>
> Using the Charmm-beta force field in directory ./charmm-beta.ff
>
> Opening force field file ./charmm-beta.ff/watermodels.dat
>
> Select the Water Model:
>  ?1: TIP3P??? TIP 3-point, recommended, by default uses CHARMM TIP3 with
> LJ on H
>  ?2: TIP4P??? TIP 4-point
>  ?3: TIP5P??? TIP 5-point
>  ?4: SPC??? ??? simple point charge
>  ?5: SPC/E??? extended simple point charge
>  ?6: Methanol?? Equilibrated methanol
>  ?7: Octanol??? Equilibrated octanol
>  ?8: None
> 1
> going to rename ./charmm-beta.ff/merged.r2b
> Opening force field file ./charmm-beta.ff/merged.r2b
> Reading 6lyz.pdb...
> WARNING: all CONECT records are ignored
> Read '', 1001 atoms
> Analyzing pdb file
> Splitting chemical chains based on TER records or chain id changing.
> There are 1 chains and 0 blocks of water and 129 residues with 1001 atoms
>
>  ? chain? #res #atoms
>  ? 1 'A'?? 129?? 1001
>
> All occupancies are one
> Opening force field file ./charmm-beta.ff/atomtypes.atp
> Opening force field file ./charmm-beta.ff/betaaminoacids.atp
> Opening force field file ./charmm-beta.ff/cyclicbeta.atp
> Reading residue database... (Charmm-beta)
> Opening force field file ./charmm-beta.ff/betaaminoacids.rtp
> Opening force field file ./charmm-beta.ff/cyclicbeta.rtp
> Opening force field file ./charmm-beta.ff/extra.rtp
> Warning: file does not end with a newline, last line:
> ;
> Opening force field file ./charmm-beta.ff/merged.rtp
> Opening force field file ./charmm-beta.ff/merged.hdb
> Opening force field file ./charmm-beta.ff/betaaminoacids.n.tdb
> Opening force field file ./charmm-beta.ff/cyclicbeta.n.tdb
> Opening force field file ./charmm-beta.ff/merged.n.tdb
> Opening force field file ./charmm-beta.ff/betaaminoacids.c.tdb
> Opening force field file ./charmm-beta.ff/cyclicbeta.c.tdb
> Opening force field file ./charmm-beta.ff/merged.c.tdb
> Processing chain 1 'A' (1001 atoms, 129 residues)
> Analysing hydrogen-bonding network for automated assignment of histidine
>  ?protonation. 213 donors and 184 acceptors were found.
> There are 262 hydrogen bonds
> Will use HISD for residue 15
> Identified residue LYS1 as a starting terminus.
> Identified residue LEU129 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Special Atom Distance matrix:
>  ??????????????????? CYS6?? MET12?? HIS15?? CYS30?? CYS64?? CYS76?? CYS80
>  ??????????????????? SG48??? SD87? NE2118?? SG238?? SG513?? SG601?? SG630
>  ?? MET12??? SD87?? 1.205
>  ?? HIS15? NE2118?? 1.804?? 0.998
>  ?? CYS30?? SG238?? 1.450?? 1.070?? 2.063
>  ?? CYS64?? SG513?? 2.873?? 1.779?? 1.755?? 2.236
>  ?? CYS76?? SG601?? 2.740?? 1.544?? 1.418?? 2.132?? 0.778
>  ?? CYS80?? SG630?? 3.006?? 1.943?? 1.892?? 2.387?? 0.200?? 0.958
>  ?? CYS94?? SG724?? 2.576?? 1.388?? 1.329?? 1.976?? 0.678?? 0.211?? 0.871
>  ? MET105?? SD799?? 1.866?? 0.933?? 1.679?? 0.896?? 1.858?? 1.483?? 2.047
>  ? CYS115?? SG889?? 1.625?? 1.099?? 2.068?? 0.204?? 2.108?? 2.005?? 2.260
>  ? CYS127?? SG981?? 0.203?? 1.089?? 1.733?? 1.332?? 2.808?? 2.631?? 2.950
>  ?????????????????? CYS94? MET105? CYS115
>  ?????????????????? SG724?? SD799?? SG889
>  ? MET105?? SD799?? 1.389
>  ? CYS115?? SG889?? 1.855?? 0.790
>  ? CYS127?? SG981?? 2.474?? 1.701?? 1.505
> Linking CYS-6 SG-48 and CYS-127 SG-981...
> Linking CYS-30 SG-238 and CYS-115 SG-889...
> Linking CYS-64 SG-513 and CYS-80 SG-630...
> Linking CYS-76 SG-601 and CYS-94 SG-724...
> Select start terminus type for LYS-1
>  ?0: Beta3NH3+
>  ?1: Beta2NH3+
>  ?2: Beta23NH3+
>  ?3: B3_NH2
>  ?4: B2_NH2
>  ?5: B23_NH2
>  ?6: 5TER
>  ?7: None
>
> (-------------------------- END of gmx output
> -----------------------------------)
>
> Information in the force field relevant to the beta-peptides is stored
> in betaaminoacids.{arn,atp,c.tdb,n.tdb,rtp} files. I have kept the
> original ones (merged.*) intact. From the output above it seems that
> pdb2gmx recognizes and loads all the relevant files (both
> betaaminoacids.* and merged.*), but only shows a selection of N-terminal
> patches from the betaaminoacids.n.tdb file. More precisely, the 5TER
> terminus is from merged.n.tdb, but the other ones before it get
> overridden by entries from betaaminoacids.n.tdb. Is there some rule in
> pdb2gmx which considers some endgroups equivalent and keeps only one? I
> have encountered it neither in the main documentation (section 5.6.5:
> pdb2gmx input files), nor in the help of gmx pdb2gmx.
>
> Could anyone point me to how I should do this correctly?

What is the source of these force field files? Based on the .tdb 
entries, it seems they do not include the "standard" patches that should 
be included with the official CHARMM force field.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From wacha.andras at ttk.hu  Thu Jan 16 14:44:13 2020
From: wacha.andras at ttk.hu (=?UTF-8?Q?Andr=c3=a1s_Ferenc_WACHA?=)
Date: Thu, 16 Jan 2020 13:44:13 -0000
Subject: [gmx-users] pdb2gmx picks up the wrong .tdb files?
In-Reply-To: <3fa389b9-ec22-aa09-d112-05cdef3e09aa@vt.edu>
References: <bb2d0e87-595d-f6e5-d471-8c8e031168e7@ttk.hu>
	<3fa389b9-ec22-aa09-d112-05cdef3e09aa@vt.edu>
Message-ID: <1224743b-d210-7c8c-4855-a22efbb336c0@ttk.hu>

Sorry, now replying to the whole list:

Dear Justin,

I have obtained the base force field from the website of the MacKerell
Lab
(http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36-jul2017.ff.tgz).
I have checked and the merged.n.tdb file is the same in my version and
in theirs.

Shouldn't pdb2gmx only use the termini databases corresponding to the
.rtp file from which the given residue has been read? I.e. if it is LYS,
found in merged.rtp, then only merged.{n,c}.tdb?

Kind regards,

Andras

On 1/16/20 2:33 PM, Justin Lemkul wrote:
>
>
> On 1/16/20 8:04 AM, Andr?s Ferenc WACHA wrote:
>> Dear fellow Gromacs users,
>>
>> I have developed an extended version of the CHARMM36m force field for
>> beta-amino acids (https://charmm-betaff.readthedocs.io,
>> https://gitlab.com/awacha/charmm-beta.ff). For beta-amino acids I found
>> pdb2gmx works well. However, if I try to use it for natural peptides and
>> proteins (e.g. 6LYZ from the PDB), the following command:
>>
>> gmx pdb2gmx -f 6LYZ.pdb, -ff charmm-beta -ter -ignh
>>
>> fails to recognize the correct termini database files. The output is the
>> following:
>>
>> (-------------------------- START of gmx output
>> -----------------------------------)
>>
>> GROMACS:????? gmx pdb2gmx, version 2020
>> Executable:
>> /opt/spack/opt/spack/linux-archrolling-skylake/gcc-9.2.0/gromacs-2020-ls53yrft6droj2ovhuzdwdufi4an4vir/bin/gmx
>>
>> Data prefix:
>> /opt/spack/opt/spack/linux-archrolling-skylake/gcc-9.2.0/gromacs-2020-ls53yrft6droj2ovhuzdwdufi4an4vir
>>
>> Working dir:? /home/wachaandras/gromacs/forcefields
>> Command line:
>> ?? gmx pdb2gmx -f 6lyz.pdb -ff charmm-beta -ter -ignh
>>
>> Using the Charmm-beta force field in directory ./charmm-beta.ff
>>
>> Opening force field file ./charmm-beta.ff/watermodels.dat
>>
>> Select the Water Model:
>> ??1: TIP3P??? TIP 3-point, recommended, by default uses CHARMM TIP3 with
>> LJ on H
>> ??2: TIP4P??? TIP 4-point
>> ??3: TIP5P??? TIP 5-point
>> ??4: SPC??? ??? simple point charge
>> ??5: SPC/E??? extended simple point charge
>> ??6: Methanol?? Equilibrated methanol
>> ??7: Octanol??? Equilibrated octanol
>> ??8: None
>> 1
>> going to rename ./charmm-beta.ff/merged.r2b
>> Opening force field file ./charmm-beta.ff/merged.r2b
>> Reading 6lyz.pdb...
>> WARNING: all CONECT records are ignored
>> Read '', 1001 atoms
>> Analyzing pdb file
>> Splitting chemical chains based on TER records or chain id changing.
>> There are 1 chains and 0 blocks of water and 129 residues with 1001
>> atoms
>>
>> ?? chain? #res #atoms
>> ?? 1 'A'?? 129?? 1001
>>
>> All occupancies are one
>> Opening force field file ./charmm-beta.ff/atomtypes.atp
>> Opening force field file ./charmm-beta.ff/betaaminoacids.atp
>> Opening force field file ./charmm-beta.ff/cyclicbeta.atp
>> Reading residue database... (Charmm-beta)
>> Opening force field file ./charmm-beta.ff/betaaminoacids.rtp
>> Opening force field file ./charmm-beta.ff/cyclicbeta.rtp
>> Opening force field file ./charmm-beta.ff/extra.rtp
>> Warning: file does not end with a newline, last line:
>> ;
>> Opening force field file ./charmm-beta.ff/merged.rtp
>> Opening force field file ./charmm-beta.ff/merged.hdb
>> Opening force field file ./charmm-beta.ff/betaaminoacids.n.tdb
>> Opening force field file ./charmm-beta.ff/cyclicbeta.n.tdb
>> Opening force field file ./charmm-beta.ff/merged.n.tdb
>> Opening force field file ./charmm-beta.ff/betaaminoacids.c.tdb
>> Opening force field file ./charmm-beta.ff/cyclicbeta.c.tdb
>> Opening force field file ./charmm-beta.ff/merged.c.tdb
>> Processing chain 1 'A' (1001 atoms, 129 residues)
>> Analysing hydrogen-bonding network for automated assignment of histidine
>> ??protonation. 213 donors and 184 acceptors were found.
>> There are 262 hydrogen bonds
>> Will use HISD for residue 15
>> Identified residue LYS1 as a starting terminus.
>> Identified residue LEU129 as a ending terminus.
>> 8 out of 8 lines of specbond.dat converted successfully
>> Special Atom Distance matrix:
>> ???????????????????? CYS6?? MET12?? HIS15?? CYS30?? CYS64?? CYS76??
>> CYS80
>> ???????????????????? SG48??? SD87? NE2118?? SG238?? SG513?? SG601??
>> SG630
>> ??? MET12??? SD87?? 1.205
>> ??? HIS15? NE2118?? 1.804?? 0.998
>> ??? CYS30?? SG238?? 1.450?? 1.070?? 2.063
>> ??? CYS64?? SG513?? 2.873?? 1.779?? 1.755?? 2.236
>> ??? CYS76?? SG601?? 2.740?? 1.544?? 1.418?? 2.132?? 0.778
>> ??? CYS80?? SG630?? 3.006?? 1.943?? 1.892?? 2.387?? 0.200?? 0.958
>> ??? CYS94?? SG724?? 2.576?? 1.388?? 1.329?? 1.976?? 0.678?? 0.211??
>> 0.871
>> ?? MET105?? SD799?? 1.866?? 0.933?? 1.679?? 0.896?? 1.858?? 1.483??
>> 2.047
>> ?? CYS115?? SG889?? 1.625?? 1.099?? 2.068?? 0.204?? 2.108?? 2.005??
>> 2.260
>> ?? CYS127?? SG981?? 0.203?? 1.089?? 1.733?? 1.332?? 2.808?? 2.631??
>> 2.950
>> ??????????????????? CYS94? MET105? CYS115
>> ??????????????????? SG724?? SD799?? SG889
>> ?? MET105?? SD799?? 1.389
>> ?? CYS115?? SG889?? 1.855?? 0.790
>> ?? CYS127?? SG981?? 2.474?? 1.701?? 1.505
>> Linking CYS-6 SG-48 and CYS-127 SG-981...
>> Linking CYS-30 SG-238 and CYS-115 SG-889...
>> Linking CYS-64 SG-513 and CYS-80 SG-630...
>> Linking CYS-76 SG-601 and CYS-94 SG-724...
>> Select start terminus type for LYS-1
>> ??0: Beta3NH3+
>> ??1: Beta2NH3+
>> ??2: Beta23NH3+
>> ??3: B3_NH2
>> ??4: B2_NH2
>> ??5: B23_NH2
>> ??6: 5TER
>> ??7: None
>>
>> (-------------------------- END of gmx output
>> -----------------------------------)
>>
>> Information in the force field relevant to the beta-peptides is stored
>> in betaaminoacids.{arn,atp,c.tdb,n.tdb,rtp} files. I have kept the
>> original ones (merged.*) intact. From the output above it seems that
>> pdb2gmx recognizes and loads all the relevant files (both
>> betaaminoacids.* and merged.*), but only shows a selection of N-terminal
>> patches from the betaaminoacids.n.tdb file. More precisely, the 5TER
>> terminus is from merged.n.tdb, but the other ones before it get
>> overridden by entries from betaaminoacids.n.tdb. Is there some rule in
>> pdb2gmx which considers some endgroups equivalent and keeps only one? I
>> have encountered it neither in the main documentation (section 5.6.5:
>> pdb2gmx input files), nor in the help of gmx pdb2gmx.
>>
>> Could anyone point me to how I should do this correctly?
>
> What is the source of these force field files? Based on the .tdb
> entries, it seems they do not include the "standard" patches that
> should be included with the official CHARMM force field.
>
> -Justin
>
-- 
Andr?s Ferenc Wacha, PhD
research fellow, CREDO instrument responsible

Biological Nanochemistry Research Group (310)

Institute of Materials and Environmental Chemistry
Research Centre for Natural Sciences (RCNS)
Magyar tud?sok k?r?tja 2.
H-1117 Budapest, Hungary
Phone: +36-1-382-6427
Web: http://bionano.ttk.hu
CREDO SAXS instrument: http://credo.ttk.hu


-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 554 bytes
Desc: OpenPGP digital signature
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20200116/5eb07e32/attachment.sig>

From jalemkul at vt.edu  Thu Jan 16 14:48:08 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Thu, 16 Jan 2020 13:48:08 -0000
Subject: [gmx-users] pdb2gmx picks up the wrong .tdb files?
In-Reply-To: <1224743b-d210-7c8c-4855-a22efbb336c0@ttk.hu>
References: <bb2d0e87-595d-f6e5-d471-8c8e031168e7@ttk.hu>
	<3fa389b9-ec22-aa09-d112-05cdef3e09aa@vt.edu>
	<1224743b-d210-7c8c-4855-a22efbb336c0@ttk.hu>
Message-ID: <e10a55fa-d20a-c779-e1c1-834044379c49@vt.edu>



On 1/16/20 8:44 AM, Andr?s Ferenc WACHA wrote:
> Sorry, now replying to the whole list:
>
> Dear Justin,
>
> I have obtained the base force field from the website of the MacKerell
> Lab
> (http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36-jul2017.ff.tgz).
> I have checked and the merged.n.tdb file is the same in my version and
> in theirs.
>
> Shouldn't pdb2gmx only use the termini databases corresponding to the
> .rtp file from which the given residue has been read? I.e. if it is LYS,
> found in merged.rtp, then only merged.{n,c}.tdb?

The base names should match between .rtp and .tdb but I have never tried 
having multiple types of protein residues in different files.

-Justin

> Kind regards,
>
> Andras
>
> On 1/16/20 2:33 PM, Justin Lemkul wrote:
>>
>> On 1/16/20 8:04 AM, Andr?s Ferenc WACHA wrote:
>>> Dear fellow Gromacs users,
>>>
>>> I have developed an extended version of the CHARMM36m force field for
>>> beta-amino acids (https://charmm-betaff.readthedocs.io,
>>> https://gitlab.com/awacha/charmm-beta.ff). For beta-amino acids I found
>>> pdb2gmx works well. However, if I try to use it for natural peptides and
>>> proteins (e.g. 6LYZ from the PDB), the following command:
>>>
>>> gmx pdb2gmx -f 6LYZ.pdb, -ff charmm-beta -ter -ignh
>>>
>>> fails to recognize the correct termini database files. The output is the
>>> following:
>>>
>>> (-------------------------- START of gmx output
>>> -----------------------------------)
>>>
>>> GROMACS:????? gmx pdb2gmx, version 2020
>>> Executable:
>>> /opt/spack/opt/spack/linux-archrolling-skylake/gcc-9.2.0/gromacs-2020-ls53yrft6droj2ovhuzdwdufi4an4vir/bin/gmx
>>>
>>> Data prefix:
>>> /opt/spack/opt/spack/linux-archrolling-skylake/gcc-9.2.0/gromacs-2020-ls53yrft6droj2ovhuzdwdufi4an4vir
>>>
>>> Working dir:? /home/wachaandras/gromacs/forcefields
>>> Command line:
>>>  ?? gmx pdb2gmx -f 6lyz.pdb -ff charmm-beta -ter -ignh
>>>
>>> Using the Charmm-beta force field in directory ./charmm-beta.ff
>>>
>>> Opening force field file ./charmm-beta.ff/watermodels.dat
>>>
>>> Select the Water Model:
>>>  ??1: TIP3P??? TIP 3-point, recommended, by default uses CHARMM TIP3 with
>>> LJ on H
>>>  ??2: TIP4P??? TIP 4-point
>>>  ??3: TIP5P??? TIP 5-point
>>>  ??4: SPC??? ??? simple point charge
>>>  ??5: SPC/E??? extended simple point charge
>>>  ??6: Methanol?? Equilibrated methanol
>>>  ??7: Octanol??? Equilibrated octanol
>>>  ??8: None
>>> 1
>>> going to rename ./charmm-beta.ff/merged.r2b
>>> Opening force field file ./charmm-beta.ff/merged.r2b
>>> Reading 6lyz.pdb...
>>> WARNING: all CONECT records are ignored
>>> Read '', 1001 atoms
>>> Analyzing pdb file
>>> Splitting chemical chains based on TER records or chain id changing.
>>> There are 1 chains and 0 blocks of water and 129 residues with 1001
>>> atoms
>>>
>>>  ?? chain? #res #atoms
>>>  ?? 1 'A'?? 129?? 1001
>>>
>>> All occupancies are one
>>> Opening force field file ./charmm-beta.ff/atomtypes.atp
>>> Opening force field file ./charmm-beta.ff/betaaminoacids.atp
>>> Opening force field file ./charmm-beta.ff/cyclicbeta.atp
>>> Reading residue database... (Charmm-beta)
>>> Opening force field file ./charmm-beta.ff/betaaminoacids.rtp
>>> Opening force field file ./charmm-beta.ff/cyclicbeta.rtp
>>> Opening force field file ./charmm-beta.ff/extra.rtp
>>> Warning: file does not end with a newline, last line:
>>> ;
>>> Opening force field file ./charmm-beta.ff/merged.rtp
>>> Opening force field file ./charmm-beta.ff/merged.hdb
>>> Opening force field file ./charmm-beta.ff/betaaminoacids.n.tdb
>>> Opening force field file ./charmm-beta.ff/cyclicbeta.n.tdb
>>> Opening force field file ./charmm-beta.ff/merged.n.tdb
>>> Opening force field file ./charmm-beta.ff/betaaminoacids.c.tdb
>>> Opening force field file ./charmm-beta.ff/cyclicbeta.c.tdb
>>> Opening force field file ./charmm-beta.ff/merged.c.tdb
>>> Processing chain 1 'A' (1001 atoms, 129 residues)
>>> Analysing hydrogen-bonding network for automated assignment of histidine
>>>  ??protonation. 213 donors and 184 acceptors were found.
>>> There are 262 hydrogen bonds
>>> Will use HISD for residue 15
>>> Identified residue LYS1 as a starting terminus.
>>> Identified residue LEU129 as a ending terminus.
>>> 8 out of 8 lines of specbond.dat converted successfully
>>> Special Atom Distance matrix:
>>>  ???????????????????? CYS6?? MET12?? HIS15?? CYS30?? CYS64?? CYS76
>>> CYS80
>>>  ???????????????????? SG48??? SD87? NE2118?? SG238?? SG513?? SG601
>>> SG630
>>>  ??? MET12??? SD87?? 1.205
>>>  ??? HIS15? NE2118?? 1.804?? 0.998
>>>  ??? CYS30?? SG238?? 1.450?? 1.070?? 2.063
>>>  ??? CYS64?? SG513?? 2.873?? 1.779?? 1.755?? 2.236
>>>  ??? CYS76?? SG601?? 2.740?? 1.544?? 1.418?? 2.132?? 0.778
>>>  ??? CYS80?? SG630?? 3.006?? 1.943?? 1.892?? 2.387?? 0.200?? 0.958
>>>  ??? CYS94?? SG724?? 2.576?? 1.388?? 1.329?? 1.976?? 0.678?? 0.211
>>> 0.871
>>>  ?? MET105?? SD799?? 1.866?? 0.933?? 1.679?? 0.896?? 1.858?? 1.483
>>> 2.047
>>>  ?? CYS115?? SG889?? 1.625?? 1.099?? 2.068?? 0.204?? 2.108?? 2.005
>>> 2.260
>>>  ?? CYS127?? SG981?? 0.203?? 1.089?? 1.733?? 1.332?? 2.808?? 2.631
>>> 2.950
>>>  ??????????????????? CYS94? MET105? CYS115
>>>  ??????????????????? SG724?? SD799?? SG889
>>>  ?? MET105?? SD799?? 1.389
>>>  ?? CYS115?? SG889?? 1.855?? 0.790
>>>  ?? CYS127?? SG981?? 2.474?? 1.701?? 1.505
>>> Linking CYS-6 SG-48 and CYS-127 SG-981...
>>> Linking CYS-30 SG-238 and CYS-115 SG-889...
>>> Linking CYS-64 SG-513 and CYS-80 SG-630...
>>> Linking CYS-76 SG-601 and CYS-94 SG-724...
>>> Select start terminus type for LYS-1
>>>  ??0: Beta3NH3+
>>>  ??1: Beta2NH3+
>>>  ??2: Beta23NH3+
>>>  ??3: B3_NH2
>>>  ??4: B2_NH2
>>>  ??5: B23_NH2
>>>  ??6: 5TER
>>>  ??7: None
>>>
>>> (-------------------------- END of gmx output
>>> -----------------------------------)
>>>
>>> Information in the force field relevant to the beta-peptides is stored
>>> in betaaminoacids.{arn,atp,c.tdb,n.tdb,rtp} files. I have kept the
>>> original ones (merged.*) intact. From the output above it seems that
>>> pdb2gmx recognizes and loads all the relevant files (both
>>> betaaminoacids.* and merged.*), but only shows a selection of N-terminal
>>> patches from the betaaminoacids.n.tdb file. More precisely, the 5TER
>>> terminus is from merged.n.tdb, but the other ones before it get
>>> overridden by entries from betaaminoacids.n.tdb. Is there some rule in
>>> pdb2gmx which considers some endgroups equivalent and keeps only one? I
>>> have encountered it neither in the main documentation (section 5.6.5:
>>> pdb2gmx input files), nor in the help of gmx pdb2gmx.
>>>
>>> Could anyone point me to how I should do this correctly?
>> What is the source of these force field files? Based on the .tdb
>> entries, it seems they do not include the "standard" patches that
>> should be included with the official CHARMM force field.
>>
>> -Justin
>>
>>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From nicolas.cheron.boulot at gmail.com  Thu Jan 16 15:59:00 2020
From: nicolas.cheron.boulot at gmail.com (Nicolas Cheron)
Date: Thu, 16 Jan 2020 14:59:00 -0000
Subject: [gmx-users] solute tempering (REST2)
In-Reply-To: <DB8PR10MB2649D76668D34899D1E14ABAEA3A0@DB8PR10MB2649.EURPRD10.PROD.OUTLOOK.COM>
References: <DB8PR10MB2649D76668D34899D1E14ABAEA3A0@DB8PR10MB2649.EURPRD10.PROD.OUTLOOK.COM>
Message-ID: <CAA5k+evkBe=LtqxdhoWpZmNAd2gGorZ_Lkz0tiM=HET0hQd0dw@mail.gmail.com>

Hi,

You can patch Gromacs with Plumed and use hrex:
* generate a full .top file of your system (with -pp in the grompp command)
* open your .top and add "_" in the second column (type) of each atom you
want to apply REST2 in the [ atoms ] section  of the moleculetype
* use the command "plumed partial_tempering ..." as described in
https://www.plumed.org/doc-v2.5/user-doc/html/hrex.html to create all the
scaled topologies
* use grompp to generate all the tpr
* run gromacs. The website above suggest the use of multi which doesn't
work anymore. Something like this should work "gmx mdrun -multidir run0
run1 run2 run3 -deffnm NPT -plumed Plumed.dat -replex 200 -hrex" (where you
have created the folders run0, run1, run2 and run3, and in each one there
is the corresponding file NPT.tpr). You need the file Plumed.dat even if it
can be empty

Nicolas


Le dim. 12 janv. 2020 ? 23:02, hind ahmed <aa.hind at hotmail.com> a ?crit :

> Dear All,
> Is there a tutorial for solute tempering (REST2) in gromacs or any clear
> guide to apply this method?
>
> Regards,
>
> Thank you
>
> Sent from my Huawei tablet
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From nicolas.cheron.boulot at gmail.com  Thu Jan 16 15:59:01 2020
From: nicolas.cheron.boulot at gmail.com (Nicolas Cheron)
Date: Thu, 16 Jan 2020 14:59:01 -0000
Subject: [gmx-users] solute tempering (REST2)
In-Reply-To: <DB8PR10MB2649D76668D34899D1E14ABAEA3A0@DB8PR10MB2649.EURPRD10.PROD.OUTLOOK.COM>
References: <DB8PR10MB2649D76668D34899D1E14ABAEA3A0@DB8PR10MB2649.EURPRD10.PROD.OUTLOOK.COM>
Message-ID: <CAA5k+evkBe=LtqxdhoWpZmNAd2gGorZ_Lkz0tiM=HET0hQd0dw@mail.gmail.com>

Hi,

You can patch Gromacs with Plumed and use hrex:
* generate a full .top file of your system (with -pp in the grompp command)
* open your .top and add "_" in the second column (type) of each atom you
want to apply REST2 in the [ atoms ] section  of the moleculetype
* use the command "plumed partial_tempering ..." as described in
https://www.plumed.org/doc-v2.5/user-doc/html/hrex.html to create all the
scaled topologies
* use grompp to generate all the tpr
* run gromacs. The website above suggest the use of multi which doesn't
work anymore. Something like this should work "gmx mdrun -multidir run0
run1 run2 run3 -deffnm NPT -plumed Plumed.dat -replex 200 -hrex" (where you
have created the folders run0, run1, run2 and run3, and in each one there
is the corresponding file NPT.tpr). You need the file Plumed.dat even if it
can be empty

Nicolas


Le dim. 12 janv. 2020 ? 23:02, hind ahmed <aa.hind at hotmail.com> a ?crit :

> Dear All,
> Is there a tutorial for solute tempering (REST2) in gromacs or any clear
> guide to apply this method?
>
> Regards,
>
> Thank you
>
> Sent from my Huawei tablet
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From wacha.andras at ttk.hu  Thu Jan 16 16:07:56 2020
From: wacha.andras at ttk.hu (=?UTF-8?Q?Andr=c3=a1s_Ferenc_WACHA?=)
Date: Thu, 16 Jan 2020 15:07:56 -0000
Subject: [gmx-users] pdb2gmx picks up the wrong .tdb files?
In-Reply-To: <e10a55fa-d20a-c779-e1c1-834044379c49@vt.edu>
References: <bb2d0e87-595d-f6e5-d471-8c8e031168e7@ttk.hu>
	<3fa389b9-ec22-aa09-d112-05cdef3e09aa@vt.edu>
	<1224743b-d210-7c8c-4855-a22efbb336c0@ttk.hu>
	<e10a55fa-d20a-c779-e1c1-834044379c49@vt.edu>
Message-ID: <4f683b2f-0fad-c0cc-92f0-a45a2d91e784@ttk.hu>

Dear Justin,

thank you. Am I doing something wrong or is this a bug in Gromacs? Do
you have a suggestion how to make this work? Should I rename the
terminal patches or should I put everything under one basename
(sacrificing cleanliness and maintainability)?

Kind regards,

Andras

On 1/16/20 2:47 PM, Justin Lemkul wrote:

>
>
> On 1/16/20 8:44 AM, Andr?s Ferenc WACHA wrote:
>> Sorry, now replying to the whole list:
>>
>> Dear Justin,
>>
>> I have obtained the base force field from the website of the MacKerell
>> Lab
>> (http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36-jul2017.ff.tgz).
>> I have checked and the merged.n.tdb file is the same in my version and
>> in theirs.
>>
>> Shouldn't pdb2gmx only use the termini databases corresponding to the
>> .rtp file from which the given residue has been read? I.e. if it is LYS,
>> found in merged.rtp, then only merged.{n,c}.tdb?
>
> The base names should match between .rtp and .tdb but I have never
> tried having multiple types of protein residues in different files.
>
> -Justin
>
>> Kind regards,
>>
>> Andras
>>
>> On 1/16/20 2:33 PM, Justin Lemkul wrote:
>>> On 1/16/20 8:04 AM, Andr?s Ferenc WACHA wrote:
>>>> Dear fellow Gromacs users,
>>>>
>>>> I have developed an extended version of the CHARMM36m force field for
>>>> beta-amino acids (https://charmm-betaff.readthedocs.io,
>>>> https://gitlab.com/awacha/charmm-beta.ff). For beta-amino acids I found
>>>> pdb2gmx works well. However, if I try to use it for natural peptides and
>>>> proteins (e.g. 6LYZ from the PDB), the following command:
>>>>
>>>> gmx pdb2gmx -f 6LYZ.pdb, -ff charmm-beta -ter -ignh
>>>>
>>>> fails to recognize the correct termini database files. The output is the
>>>> following:
>>>>
>>>> (-------------------------- START of gmx output
>>>> -----------------------------------)
>>>>
>>>> GROMACS:????? gmx pdb2gmx, version 2020
>>>> Executable:
>>>> /opt/spack/opt/spack/linux-archrolling-skylake/gcc-9.2.0/gromacs-2020-ls53yrft6droj2ovhuzdwdufi4an4vir/bin/gmx
>>>>
>>>> Data prefix:
>>>> /opt/spack/opt/spack/linux-archrolling-skylake/gcc-9.2.0/gromacs-2020-ls53yrft6droj2ovhuzdwdufi4an4vir
>>>>
>>>> Working dir:? /home/wachaandras/gromacs/forcefields
>>>> Command line:
>>>> ?? gmx pdb2gmx -f 6lyz.pdb -ff charmm-beta -ter -ignh
>>>>
>>>> Using the Charmm-beta force field in directory ./charmm-beta.ff
>>>>
>>>> Opening force field file ./charmm-beta.ff/watermodels.dat
>>>>
>>>> Select the Water Model:
>>>> ??1: TIP3P??? TIP 3-point, recommended, by default uses CHARMM TIP3 with
>>>> LJ on H
>>>> ??2: TIP4P??? TIP 4-point
>>>> ??3: TIP5P??? TIP 5-point
>>>> ??4: SPC??? ??? simple point charge
>>>> ??5: SPC/E??? extended simple point charge
>>>> ??6: Methanol?? Equilibrated methanol
>>>> ??7: Octanol??? Equilibrated octanol
>>>> ??8: None
>>>> 1
>>>> going to rename ./charmm-beta.ff/merged.r2b
>>>> Opening force field file ./charmm-beta.ff/merged.r2b
>>>> Reading 6lyz.pdb...
>>>> WARNING: all CONECT records are ignored
>>>> Read '', 1001 atoms
>>>> Analyzing pdb file
>>>> Splitting chemical chains based on TER records or chain id changing.
>>>> There are 1 chains and 0 blocks of water and 129 residues with 1001
>>>> atoms
>>>>
>>>> ?? chain? #res #atoms
>>>> ?? 1 'A'?? 129?? 1001
>>>>
>>>> All occupancies are one
>>>> Opening force field file ./charmm-beta.ff/atomtypes.atp
>>>> Opening force field file ./charmm-beta.ff/betaaminoacids.atp
>>>> Opening force field file ./charmm-beta.ff/cyclicbeta.atp
>>>> Reading residue database... (Charmm-beta)
>>>> Opening force field file ./charmm-beta.ff/betaaminoacids.rtp
>>>> Opening force field file ./charmm-beta.ff/cyclicbeta.rtp
>>>> Opening force field file ./charmm-beta.ff/extra.rtp
>>>> Warning: file does not end with a newline, last line:
>>>> ;
>>>> Opening force field file ./charmm-beta.ff/merged.rtp
>>>> Opening force field file ./charmm-beta.ff/merged.hdb
>>>> Opening force field file ./charmm-beta.ff/betaaminoacids.n.tdb
>>>> Opening force field file ./charmm-beta.ff/cyclicbeta.n.tdb
>>>> Opening force field file ./charmm-beta.ff/merged.n.tdb
>>>> Opening force field file ./charmm-beta.ff/betaaminoacids.c.tdb
>>>> Opening force field file ./charmm-beta.ff/cyclicbeta.c.tdb
>>>> Opening force field file ./charmm-beta.ff/merged.c.tdb
>>>> Processing chain 1 'A' (1001 atoms, 129 residues)
>>>> Analysing hydrogen-bonding network for automated assignment of histidine
>>>> ??protonation. 213 donors and 184 acceptors were found.
>>>> There are 262 hydrogen bonds
>>>> Will use HISD for residue 15
>>>> Identified residue LYS1 as a starting terminus.
>>>> Identified residue LEU129 as a ending terminus.
>>>> 8 out of 8 lines of specbond.dat converted successfully
>>>> Special Atom Distance matrix:
>>>> ???????????????????? CYS6?? MET12?? HIS15?? CYS30?? CYS64?? CYS76??
>>>> CYS80
>>>> ???????????????????? SG48??? SD87? NE2118?? SG238?? SG513?? SG601??
>>>> SG630
>>>> ??? MET12??? SD87?? 1.205
>>>> ??? HIS15? NE2118?? 1.804?? 0.998
>>>> ??? CYS30?? SG238?? 1.450?? 1.070?? 2.063
>>>> ??? CYS64?? SG513?? 2.873?? 1.779?? 1.755?? 2.236
>>>> ??? CYS76?? SG601?? 2.740?? 1.544?? 1.418?? 2.132?? 0.778
>>>> ??? CYS80?? SG630?? 3.006?? 1.943?? 1.892?? 2.387?? 0.200?? 0.958
>>>> ??? CYS94?? SG724?? 2.576?? 1.388?? 1.329?? 1.976?? 0.678?? 0.211??
>>>> 0.871
>>>> ?? MET105?? SD799?? 1.866?? 0.933?? 1.679?? 0.896?? 1.858?? 1.483??
>>>> 2.047
>>>> ?? CYS115?? SG889?? 1.625?? 1.099?? 2.068?? 0.204?? 2.108?? 2.005??
>>>> 2.260
>>>> ?? CYS127?? SG981?? 0.203?? 1.089?? 1.733?? 1.332?? 2.808?? 2.631??
>>>> 2.950
>>>> ??????????????????? CYS94? MET105? CYS115
>>>> ??????????????????? SG724?? SD799?? SG889
>>>> ?? MET105?? SD799?? 1.389
>>>> ?? CYS115?? SG889?? 1.855?? 0.790
>>>> ?? CYS127?? SG981?? 2.474?? 1.701?? 1.505
>>>> Linking CYS-6 SG-48 and CYS-127 SG-981...
>>>> Linking CYS-30 SG-238 and CYS-115 SG-889...
>>>> Linking CYS-64 SG-513 and CYS-80 SG-630...
>>>> Linking CYS-76 SG-601 and CYS-94 SG-724...
>>>> Select start terminus type for LYS-1
>>>> ??0: Beta3NH3+
>>>> ??1: Beta2NH3+
>>>> ??2: Beta23NH3+
>>>> ??3: B3_NH2
>>>> ??4: B2_NH2
>>>> ??5: B23_NH2
>>>> ??6: 5TER
>>>> ??7: None
>>>>
>>>> (-------------------------- END of gmx output
>>>> -----------------------------------)
>>>>
>>>> Information in the force field relevant to the beta-peptides is stored
>>>> in betaaminoacids.{arn,atp,c.tdb,n.tdb,rtp} files. I have kept the
>>>> original ones (merged.*) intact. From the output above it seems that
>>>> pdb2gmx recognizes and loads all the relevant files (both
>>>> betaaminoacids.* and merged.*), but only shows a selection of N-terminal
>>>> patches from the betaaminoacids.n.tdb file. More precisely, the 5TER
>>>> terminus is from merged.n.tdb, but the other ones before it get
>>>> overridden by entries from betaaminoacids.n.tdb. Is there some rule in
>>>> pdb2gmx which considers some endgroups equivalent and keeps only one? I
>>>> have encountered it neither in the main documentation (section 5.6.5:
>>>> pdb2gmx input files), nor in the help of gmx pdb2gmx.
>>>>
>>>> Could anyone point me to how I should do this correctly?
>>> What is the source of these force field files? Based on the .tdb
>>> entries, it seems they do not include the "standard" patches that
>>> should be included with the official CHARMM force field.
>>>
>>> -Justin
>>>
>>>
>
> -- 
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================

-- 
Andr?s Ferenc Wacha, PhD
research fellow, CREDO instrument responsible

Biological Nanochemistry Research Group (310)

Institute of Materials and Environmental Chemistry
Research Centre for Natural Sciences (RCNS)
Magyar tud?sok k?r?tja 2.
H-1117 Budapest, Hungary
Phone: +36-1-382-6427
Web: http://bionano.ttk.hu
CREDO SAXS instrument: http://credo.ttk.hu

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20200116/3531b676/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 554 bytes
Desc: OpenPGP digital signature
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20200116/3531b676/attachment-0001.sig>

From dkozuch at princeton.edu  Thu Jan 16 16:48:29 2020
From: dkozuch at princeton.edu (Daniel Kozuch)
Date: Thu, 16 Jan 2020 15:48:29 -0000
Subject: [gmx-users] Lambda Weights from Expanded Ensemble Code
In-Reply-To: <CA+zJb=j70oxwOFRqAVrnyHsk4rnW++b9ydibY_ggjY3ks53szg@mail.gmail.com>
References: <CAOKxWzJb8aUpQD5f6s_hAXp7cUOivRrO_BShJPxTWcuGnH9kQA@mail.gmail.com>
	<CA+zJb=j70oxwOFRqAVrnyHsk4rnW++b9ydibY_ggjY3ks53szg@mail.gmail.com>
Message-ID: <CAOKxWzLzDBVYUz-Z6wN+ToA4wUauy=-8PBZTPdcN7GzaDtZ=uQ@mail.gmail.com>

Okay, thanks, I created a redmine request: #3304

On Wed, Jan 15, 2020 at 11:23 PM Michael Shirts <mrshirts at gmail.com> wrote:

> The simulated tempering options haven't been as well tested as the
> hamiltonian expanded ensemble version.  The weights SHOULD be showing up in
> the column that says -nan, but clearly they aren't.  If you file a redmine
> issue, I may be able to take a look, but it might take a while to address.
>
> On Wed, Jan 15, 2020 at 8:52 PM Daniel Kozuch <dkozuch at princeton.edu>
> wrote:
>
> > Hello,
> >
> > I am interested in using simulated tempering in GROMACS (2019.5) under
> the
> > expanded ensemble options. Is there a way to monitor the ensemble weights
> > as the simulation progresses? I think in theory they are supposed to be
> > printed out in the log file, but it is only printing 0, -nan, and inf:
> >
> >             MC-lambda information
> >   N  Temp.(K)    Count   G(in kT)  dG(in kT)
> > ...
> >  36  359.105      118       -nan       -nan <<
> >  37  366.880       96       -nan       -nan
> >  38  374.852      107       -nan       -nan
> >  39  383.026      129       -nan       -nan
> >  40  391.407      166       -nan       -nan
> >  41  400.000      199       -nan    0.00000
> >
> > Here are my relevant mdp settings:
> > simulated-tempering             = yes
> > nstexpanded                     = 500
> > simulated-tempering-scaling     = exponential
> > lmc-stats                       = metropolis-transition
> > lmc-move                        = metropolis
> >
> > Any suggestions?
> >
> > Best,
> > Dan Kozuch
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From deligkaris at gmail.com  Thu Jan 16 17:04:08 2020
From: deligkaris at gmail.com (Christos Deligkaris)
Date: Thu, 16 Jan 2020 16:04:08 -0000
Subject: [gmx-users] com motion and position restraints may cause
	artifacts
In-Reply-To: <d2752133-25de-0e26-1266-4c5f599e0122@vt.edu>
References: <CAAHQ3wkvyk9UmO_5=YYEVQLhtetEEVwqVXp-jyEY55DgW-sRqg@mail.gmail.com>
	<CANogp5wm2T7QDHG5wpw16PBqqXvBU=YKUckdAT5a4-k-+JMmyQ@mail.gmail.com>
	<d2752133-25de-0e26-1266-4c5f599e0122@vt.edu>
Message-ID: <CAAHQ3w=RK5QuyAV733+nK0A3N09BGEnZPie=QH3tS+9tS+-6Nw@mail.gmail.com>

The ambiguity in the gromacs 2020 note made me concerned, as it was
not clear to me whether my system (DNA+small molecule) fills in the
category where artifacts are caused. The gromacs note could have been
a bit more helpful by referencing specific publications so that we can
educate ourselves.....

Best wishes,

Christos Deligkaris, PhD

On Thu, Jan 16, 2020 at 5:21 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> On 1/16/20 5:17 AM, Alessandra Villa wrote:
> > Hi,
> >
> > On Mon, Jan 13, 2020 at 3:36 PM Christos Deligkaris <deligkaris at gmail.com>
> > wrote:
> >
> >> dear all,
> >>
> >> I installed gromacs 2020 and I now get the following message during
> >> equilibration:
> >>
> >> NOTE 1 [file nvt.mdp]:
> >>
> >>    Removing center of mass motion in the presence of position
> >> restraints  might cause artifacts
> >>
> >> I do not recall seeing this with gromacs 2018. In which cases are
> >> artifacts created? Is it now recommended to not remove the center of
> >> mass motion during equilibration?
> >>
> >>
> > It is recommended not to have position restrain and remove of center of
> > mass at the same moment. That is also the case of the equilibration phase.
> > That may cause artifact depending on the system and the condition you are
> > simulating.
>
> What is the nature of these artifacts and where is this documented?
> Combining position restraints with COM motion removal is an extremely
> common practice. Phrases like "might cause artifacts" are troubling
> because that implies uncertainty. Are there cases when this combination
> does not cause artifacts?
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

From rabetayeasmin at gmail.com  Thu Jan 16 17:37:14 2020
From: rabetayeasmin at gmail.com (Rabeta Yeasmin)
Date: Thu, 16 Jan 2020 16:37:14 -0000
Subject: [gmx-users] Calculating C-alpha RMSD for coarse grained
	simulation
Message-ID: <CAB5hSovBCzLgQb-kjBNMTyg_XszXGeSd3LximgnM5kXFitqJDg@mail.gmail.com>

Hi Bhupendra,

Thanks for your reply. The RMSD is actually 3.5nm means 35A, which seems
very large compared to the RMSD of that protein in all-atom simulation
which is mostly between 5-6A. I have checked the trajectory as you
suggested, My system is a dimer protein inside a lipid bilayer and it looks
like if I remove the pbc effect using the following command
*gmx trjconv -s 0A.gro -f 0A-2.xtc -o 0A-2-pbc.xtc -pbc nojump -ur compact
-n index-all.ndx*

the protein structure get stretched all the time  which causes the RMSD to
be so high all-the time. If I use the original trajectory, the RMSD is
usually 0.9nm to 1.5nm except when the protein encounter pbc effect. I am
wondering how can I remove pbc effect without stretching the protein and
keeping the dimer as a whole.

Thanks.
Rabeta Yeasmin

From rabetayeasmin at gmail.com  Thu Jan 16 17:37:14 2020
From: rabetayeasmin at gmail.com (Rabeta Yeasmin)
Date: Thu, 16 Jan 2020 16:37:14 -0000
Subject: [gmx-users] Calculating C-alpha RMSD for coarse grained
	simulation
Message-ID: <CAB5hSovBCzLgQb-kjBNMTyg_XszXGeSd3LximgnM5kXFitqJDg@mail.gmail.com>

Hi Bhupendra,

Thanks for your reply. The RMSD is actually 3.5nm means 35A, which seems
very large compared to the RMSD of that protein in all-atom simulation
which is mostly between 5-6A. I have checked the trajectory as you
suggested, My system is a dimer protein inside a lipid bilayer and it looks
like if I remove the pbc effect using the following command
*gmx trjconv -s 0A.gro -f 0A-2.xtc -o 0A-2-pbc.xtc -pbc nojump -ur compact
-n index-all.ndx*

the protein structure get stretched all the time  which causes the RMSD to
be so high all-the time. If I use the original trajectory, the RMSD is
usually 0.9nm to 1.5nm except when the protein encounter pbc effect. I am
wondering how can I remove pbc effect without stretching the protein and
keeping the dimer as a whole.

Thanks.
Rabeta Yeasmin

From bhupendra.dandekar001 at gmail.com  Thu Jan 16 17:46:11 2020
From: bhupendra.dandekar001 at gmail.com (Bhupendra Dandekar)
Date: Thu, 16 Jan 2020 16:46:11 -0000
Subject: [gmx-users] Calculating C-alpha RMSD for coarse grained
	simulation
In-Reply-To: <CAB5hSovBCzLgQb-kjBNMTyg_XszXGeSd3LximgnM5kXFitqJDg@mail.gmail.com>
References: <CAB5hSovBCzLgQb-kjBNMTyg_XszXGeSd3LximgnM5kXFitqJDg@mail.gmail.com>
Message-ID: <CA+jgKGVdL3oXjW=jcsq-zx_TijpfBm26XcL7aYYyLKk7DBCRWg@mail.gmail.com>

I will look into this and get back to you again. But meanwhile just try
using .tpr file instead of.gro file in your pbc correction step.

Thanks
Bhupendra

On Thu, Jan 16, 2020, 10:07 PM Rabeta Yeasmin <rabetayeasmin at gmail.com>
wrote:

> Hi Bhupendra,
>
> Thanks for your reply. The RMSD is actually 3.5nm means 35A, which seems
> very large compared to the RMSD of that protein in all-atom simulation
> which is mostly between 5-6A. I have checked the trajectory as you
> suggested, My system is a dimer protein inside a lipid bilayer and it looks
> like if I remove the pbc effect using the following command
> *gmx trjconv -s 0A.gro -f 0A-2.xtc -o 0A-2-pbc.xtc -pbc nojump -ur compact
> -n index-all.ndx*
>
> the protein structure get stretched all the time  which causes the RMSD to
> be so high all-the time. If I use the original trajectory, the RMSD is
> usually 0.9nm to 1.5nm except when the protein encounter pbc effect. I am
> wondering how can I remove pbc effect without stretching the protein and
> keeping the dimer as a whole.
>
> Thanks.
> Rabeta Yeasmin
>
>

From bhupendra.dandekar001 at gmail.com  Thu Jan 16 17:46:11 2020
From: bhupendra.dandekar001 at gmail.com (Bhupendra Dandekar)
Date: Thu, 16 Jan 2020 16:46:11 -0000
Subject: [gmx-users] Calculating C-alpha RMSD for coarse grained
	simulation
In-Reply-To: <CAB5hSovBCzLgQb-kjBNMTyg_XszXGeSd3LximgnM5kXFitqJDg@mail.gmail.com>
References: <CAB5hSovBCzLgQb-kjBNMTyg_XszXGeSd3LximgnM5kXFitqJDg@mail.gmail.com>
Message-ID: <CA+jgKGVdL3oXjW=jcsq-zx_TijpfBm26XcL7aYYyLKk7DBCRWg@mail.gmail.com>

I will look into this and get back to you again. But meanwhile just try
using .tpr file instead of.gro file in your pbc correction step.

Thanks
Bhupendra

On Thu, Jan 16, 2020, 10:07 PM Rabeta Yeasmin <rabetayeasmin at gmail.com>
wrote:

> Hi Bhupendra,
>
> Thanks for your reply. The RMSD is actually 3.5nm means 35A, which seems
> very large compared to the RMSD of that protein in all-atom simulation
> which is mostly between 5-6A. I have checked the trajectory as you
> suggested, My system is a dimer protein inside a lipid bilayer and it looks
> like if I remove the pbc effect using the following command
> *gmx trjconv -s 0A.gro -f 0A-2.xtc -o 0A-2-pbc.xtc -pbc nojump -ur compact
> -n index-all.ndx*
>
> the protein structure get stretched all the time  which causes the RMSD to
> be so high all-the time. If I use the original trajectory, the RMSD is
> usually 0.9nm to 1.5nm except when the protein encounter pbc effect. I am
> wondering how can I remove pbc effect without stretching the protein and
> keeping the dimer as a whole.
>
> Thanks.
> Rabeta Yeasmin
>
>

From 272699575 at qq.com  Thu Jan 16 17:58:06 2020
From: 272699575 at qq.com (=?ISO-8859-1?B?WkhBTkcgQ2hlbmc=?=)
Date: Thu, 16 Jan 2020 16:58:06 -0000
Subject: [gmx-users] Why it is run so slow in gromacs 2019.3 compared to
	VERSION 5.1.1?
In-Reply-To: <tencent_272F50F0AE937B99023CA48F383E81DD3607@qq.com>
References: <tencent_B72778E0898ACC0EDEE547065FCEEEA11706@qq.com>
	<tencent_272F50F0AE937B99023CA48F383E81DD3607@qq.com>
Message-ID: <tencent_8681571D38D249914C381EC987155FE2AE06@qq.com>

I have re-run the MD, with only 2 ps in both version. Indeed, the Version 2019 is far slower than the Version 5.1.1.


Version 2019 needs 114.111 hours to complete 1 ns, while Version 5.1.1 only needs&nbsp;6.362 hours to complete 1 ns.&nbsp;


The new logs files are at
https://github.com/lanselibai/gromacs-20200116



The MD is run on our HPC cluster. So I personally could not compile it. Is there still some way to get equivalent performance for the Version 2019?




------------------&nbsp;Original&nbsp;------------------
From:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
Date:&nbsp;Thu, Jan 16, 2020 07:58 AM
To:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;"gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se&gt;;

Subject:&nbsp;Re:Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?



Hi Justin, what kind of information should I look at in the log files? They are too big to paste here. Would it be possible if you can see them at https://github.com/lanselibai/gromacs-20200115&nbsp;?


Thank you!


------------------ Original ------------------
From:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
Date:&nbsp;Thu, Jan 16, 2020 03:38 AM
To:&nbsp;"gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se&gt;;
Cc:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
Subject:&nbsp;Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?



I have a nearly identical run using the "VERSION 2019.3" compared to my previous "VERSION 5.1.1". Everything during the preparation is the same except "-r" needs to be added in the "VERSION 2019.3". So "-r em.gro", "-r nvt.gro" and "-r npt.gro" are added in the grompp commands for NVT, NPT and production run, respectively.


Using "-pe mpi 12" (i.e. 12 nodes) per hour, only 5-7 ps can be processed in the "VERSION 2019.3", while 200 ps can be achieved in the "VERSION 5.1.1". Can I ask is this normal? Is there some configuration I can do in the "VERSION 2019.3" so as to accelerate the MD? 


I follow Justin's tutorial at http://www.mdtutorials.com/gmx/lysozyme/index.html
The commands I used are listed below.


gmx pdb2gmx&nbsp; -f Fab.pdb -o Fab_processed.gro -water spce&nbsp; -inter&nbsp; -ignh -merge interactive
gmx editconf -f Fab_processed.gro -o Fab_newbox.gro -c -d 1.0 -bt cubic
gmx solvate -cp Fab_newbox.gro -cs spc216.gro -o Fab_solv.gro -p topol.top
gmx grompp -f ions.mdp -c Fab_solv.gro -p topol.top -o ions.tpr -maxwarn 1 
gmx genion -s ions.tpr -o Fab_solv_ions.gro -p topol.top -pname NA -nname CL -nn 31 -neutral -conc 0.05
(Afterwards, using the HPC to run)
gmx grompp -f minim.mdp -c Fab_solv_ions.gro -p topol.top -o em.tpr
gerun mdrun_mpi -v -deffnm em
gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -r em.gro
gerun mdrun_mpi -deffnm nvt
gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -r nvt.gro
gerun mdrun_mpi -deffnm npt
gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -r npt.gro
gmx mdrun -deffnm md_0_1 -cpi -append

From del-sorbo at ill.fr  Thu Jan 16 18:53:24 2020
From: del-sorbo at ill.fr (Giuseppe R Del Sorbo)
Date: Thu, 16 Jan 2020 17:53:24 -0000
Subject: [gmx-users] gmx trjconv
Message-ID: <b1688dc90d986f1ee153829c322dadfc@ill.fr>

Dear users,

I might need an help with gmx trjconv.


I have a system with a lysine + a micelle attached on it and I have to 
analyse the radial spherical distribution on the micelle.

The idea is to center the micelle and to work on it.

I used the command "gmx trjconv - cluster" to get a centered micelle and 
if I visualize it in vmd everything is fine.

Accordind with the manual I have to follow this three steps:


     1) trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster
     2) grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr
     3) trjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump

For the first two steps everything is ok, but for the last one it 
doesnt't work. Gromacs doesn't give any error, but it doesn't run.

Than I tried to write the third step without "-pbc nojump" and it works, 
but the trajectory is a mess and I can also see the lysine, when I 
should only see the micelle..

Do you have any suggestion?

Thanks a lot


Giuseppe


From rabetayeasmin at gmail.com  Thu Jan 16 23:32:05 2020
From: rabetayeasmin at gmail.com (Rabeta Yeasmin)
Date: Thu, 16 Jan 2020 22:32:05 -0000
Subject: [gmx-users] Calculating C-alpha RMSD for coarse grained
	simulation
In-Reply-To: <CA+jgKGVdL3oXjW=jcsq-zx_TijpfBm26XcL7aYYyLKk7DBCRWg@mail.gmail.com>
References: <CAB5hSovBCzLgQb-kjBNMTyg_XszXGeSd3LximgnM5kXFitqJDg@mail.gmail.com>
	<CA+jgKGVdL3oXjW=jcsq-zx_TijpfBm26XcL7aYYyLKk7DBCRWg@mail.gmail.com>
Message-ID: <CAB5hSouF5uyyFpA4C41s0nqsr96eEfZKh+kV-NRwz5r9Rc-XvA@mail.gmail.com>

Hi,

I have solved the issue. I had problem in pbc correction step. It is good
to follow some steps in order to get a good result. What I have used is
-First made the molecules as whole to remove stretching in the structures
(protein, membrane) due to pbc effect.
*gmx trjconv -s step6.0_minimization.tpr -f 0A-1.xtc -o 0A-1-pbc-whole.xtc
-pbc whole -n index-all.ndx*

But my protein is a dimer, this command made the two monomer separated.
That's why I had to cluster the two monomer after the above command.
*gmx trjconv -s step6.0_minimization.tpr -f 0A-1-pbc-whole.xtc -o
0A-1-pbc-whole-cluster.xtc -pbc cluster -n index-all-new.ndx*

I had calculated the RMSD after this, it looks reasonable now.
Thanks for suggesting to check the trajectory.

Rabeta Yeasmin

On Thu, Jan 16, 2020 at 10:46 AM Bhupendra Dandekar <
bhupendra.dandekar001 at gmail.com> wrote:

> I will look into this and get back to you again. But meanwhile just try
> using .tpr file instead of.gro file in your pbc correction step.
>
> Thanks
> Bhupendra
>
> On Thu, Jan 16, 2020, 10:07 PM Rabeta Yeasmin <rabetayeasmin at gmail.com>
> wrote:
>
>> Hi Bhupendra,
>>
>> Thanks for your reply. The RMSD is actually 3.5nm means 35A, which seems
>> very large compared to the RMSD of that protein in all-atom simulation
>> which is mostly between 5-6A. I have checked the trajectory as you
>> suggested, My system is a dimer protein inside a lipid bilayer and it looks
>> like if I remove the pbc effect using the following command
>> *gmx trjconv -s 0A.gro -f 0A-2.xtc -o 0A-2-pbc.xtc -pbc nojump -ur
>> compact -n index-all.ndx*
>>
>> the protein structure get stretched all the time  which causes the RMSD
>> to be so high all-the time. If I use the original trajectory, the RMSD is
>> usually 0.9nm to 1.5nm except when the protein encounter pbc effect. I am
>> wondering how can I remove pbc effect without stretching the protein and
>> keeping the dimer as a whole.
>>
>> Thanks.
>> Rabeta Yeasmin
>>
>>

From rabetayeasmin at gmail.com  Thu Jan 16 23:32:05 2020
From: rabetayeasmin at gmail.com (Rabeta Yeasmin)
Date: Thu, 16 Jan 2020 22:32:05 -0000
Subject: [gmx-users] Calculating C-alpha RMSD for coarse grained
	simulation
In-Reply-To: <CA+jgKGVdL3oXjW=jcsq-zx_TijpfBm26XcL7aYYyLKk7DBCRWg@mail.gmail.com>
References: <CAB5hSovBCzLgQb-kjBNMTyg_XszXGeSd3LximgnM5kXFitqJDg@mail.gmail.com>
	<CA+jgKGVdL3oXjW=jcsq-zx_TijpfBm26XcL7aYYyLKk7DBCRWg@mail.gmail.com>
Message-ID: <CAB5hSouF5uyyFpA4C41s0nqsr96eEfZKh+kV-NRwz5r9Rc-XvA@mail.gmail.com>

Hi,

I have solved the issue. I had problem in pbc correction step. It is good
to follow some steps in order to get a good result. What I have used is
-First made the molecules as whole to remove stretching in the structures
(protein, membrane) due to pbc effect.
*gmx trjconv -s step6.0_minimization.tpr -f 0A-1.xtc -o 0A-1-pbc-whole.xtc
-pbc whole -n index-all.ndx*

But my protein is a dimer, this command made the two monomer separated.
That's why I had to cluster the two monomer after the above command.
*gmx trjconv -s step6.0_minimization.tpr -f 0A-1-pbc-whole.xtc -o
0A-1-pbc-whole-cluster.xtc -pbc cluster -n index-all-new.ndx*

I had calculated the RMSD after this, it looks reasonable now.
Thanks for suggesting to check the trajectory.

Rabeta Yeasmin

On Thu, Jan 16, 2020 at 10:46 AM Bhupendra Dandekar <
bhupendra.dandekar001 at gmail.com> wrote:

> I will look into this and get back to you again. But meanwhile just try
> using .tpr file instead of.gro file in your pbc correction step.
>
> Thanks
> Bhupendra
>
> On Thu, Jan 16, 2020, 10:07 PM Rabeta Yeasmin <rabetayeasmin at gmail.com>
> wrote:
>
>> Hi Bhupendra,
>>
>> Thanks for your reply. The RMSD is actually 3.5nm means 35A, which seems
>> very large compared to the RMSD of that protein in all-atom simulation
>> which is mostly between 5-6A. I have checked the trajectory as you
>> suggested, My system is a dimer protein inside a lipid bilayer and it looks
>> like if I remove the pbc effect using the following command
>> *gmx trjconv -s 0A.gro -f 0A-2.xtc -o 0A-2-pbc.xtc -pbc nojump -ur
>> compact -n index-all.ndx*
>>
>> the protein structure get stretched all the time  which causes the RMSD
>> to be so high all-the time. If I use the original trajectory, the RMSD is
>> usually 0.9nm to 1.5nm except when the protein encounter pbc effect. I am
>> wondering how can I remove pbc effect without stretching the protein and
>> keeping the dimer as a whole.
>>
>> Thanks.
>> Rabeta Yeasmin
>>
>>

From jalemkul at vt.edu  Thu Jan 16 23:34:54 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Thu, 16 Jan 2020 22:34:54 -0000
Subject: [gmx-users] pdb2gmx picks up the wrong .tdb files?
In-Reply-To: <4f683b2f-0fad-c0cc-92f0-a45a2d91e784@ttk.hu>
References: <bb2d0e87-595d-f6e5-d471-8c8e031168e7@ttk.hu>
	<3fa389b9-ec22-aa09-d112-05cdef3e09aa@vt.edu>
	<1224743b-d210-7c8c-4855-a22efbb336c0@ttk.hu>
	<e10a55fa-d20a-c779-e1c1-834044379c49@vt.edu>
	<4f683b2f-0fad-c0cc-92f0-a45a2d91e784@ttk.hu>
Message-ID: <88435514-06b1-c1ce-fadf-757d583a39c3@vt.edu>



On 1/16/20 10:07 AM, Andr?s Ferenc WACHA wrote:
>
> Dear Justin,
>
> thank you. Am I doing something wrong or is this a bug in Gromacs? Do 
> you have a suggestion how to make this work? Should I rename the 
> terminal patches or should I put everything under one basename 
> (sacrificing cleanliness and maintainability)?
>

Without spending a long time going through the code, likely what is 
happening is pdb2gmx is loading the .rtp files in alphabetical order, 
finding the first match of LYS (which occurs in your beta-amino acid 
file) and loads the matching .tdb file - this is why alpha-amino acids 
don't work; they're interpreted as beta. The cleanest solution would 
probably be to prefix your beta-amino acids to change their residue 
names, e.g. BLYS instead of LYS in both the .rtp and coordinate files.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From jalemkul at vt.edu  Thu Jan 16 23:37:15 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Thu, 16 Jan 2020 22:37:15 -0000
Subject: [gmx-users] Why it is run so slow in gromacs 2019.3 compared to
 VERSION 5.1.1?
In-Reply-To: <tencent_8681571D38D249914C381EC987155FE2AE06@qq.com>
References: <tencent_B72778E0898ACC0EDEE547065FCEEEA11706@qq.com>
	<tencent_272F50F0AE937B99023CA48F383E81DD3607@qq.com>
	<tencent_8681571D38D249914C381EC987155FE2AE06@qq.com>
Message-ID: <b85b07f3-4111-28a5-4ac7-841fe87bb41e@vt.edu>



On 1/16/20 11:57 AM, ZHANG Cheng wrote:
> I have re-run the MD, with only 2 ps in both version. Indeed, the Version 2019 is far slower than the Version 5.1.1.
>
>
> Version 2019 needs 114.111 hours to complete 1 ns, while Version 5.1.1 only needs&nbsp;6.362 hours to complete 1 ns.&nbsp;
>
>
> The new logs files are at
> https://github.com/lanselibai/gromacs-20200116
>
>
>
> The MD is run on our HPC cluster. So I personally could not compile it. Is there still some way to get equivalent performance for the Version 2019?
>

Try assigning the same number of PP and PME ranks in each run (30/6 in 
5.1.1 and 27/9 in 2019.3). You're losing a lot of performance in 
communicating PME forces in the 2019.3 run. You may also want to try 
version 2020 to see if automatic detection has improved.

-Justin

>
>
> ------------------&nbsp;Original&nbsp;------------------
> From:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
> Date:&nbsp;Thu, Jan 16, 2020 07:58 AM
> To:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;"gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se&gt;;
>
> Subject:&nbsp;Re:Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?
>
>
>
> Hi Justin, what kind of information should I look at in the log files? They are too big to paste here. Would it be possible if you can see them at https://github.com/lanselibai/gromacs-20200115&nbsp;?
>
>
> Thank you!
>
>
> ------------------ Original ------------------
> From:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
> Date:&nbsp;Thu, Jan 16, 2020 03:38 AM
> To:&nbsp;"gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se&gt;;
> Cc:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
> Subject:&nbsp;Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?
>
>
>
> I have a nearly identical run using the "VERSION 2019.3" compared to my previous "VERSION 5.1.1". Everything during the preparation is the same except "-r" needs to be added in the "VERSION 2019.3". So "-r em.gro", "-r nvt.gro" and "-r npt.gro" are added in the grompp commands for NVT, NPT and production run, respectively.
>
>
> Using "-pe mpi 12" (i.e. 12 nodes) per hour, only 5-7 ps can be processed in the "VERSION 2019.3", while 200 ps can be achieved in the "VERSION 5.1.1". Can I ask is this normal? Is there some configuration I can do in the "VERSION 2019.3" so as to accelerate the MD?
>
>
> I follow Justin's tutorial at http://www.mdtutorials.com/gmx/lysozyme/index.html
> The commands I used are listed below.
>
>
> gmx pdb2gmx&nbsp; -f Fab.pdb -o Fab_processed.gro -water spce&nbsp; -inter&nbsp; -ignh -merge interactive
> gmx editconf -f Fab_processed.gro -o Fab_newbox.gro -c -d 1.0 -bt cubic
> gmx solvate -cp Fab_newbox.gro -cs spc216.gro -o Fab_solv.gro -p topol.top
> gmx grompp -f ions.mdp -c Fab_solv.gro -p topol.top -o ions.tpr -maxwarn 1
> gmx genion -s ions.tpr -o Fab_solv_ions.gro -p topol.top -pname NA -nname CL -nn 31 -neutral -conc 0.05
> (Afterwards, using the HPC to run)
> gmx grompp -f minim.mdp -c Fab_solv_ions.gro -p topol.top -o em.tpr
> gerun mdrun_mpi -v -deffnm em
> gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -r em.gro
> gerun mdrun_mpi -deffnm nvt
> gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -r nvt.gro
> gerun mdrun_mpi -deffnm npt
> gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -r npt.gro
> gmx mdrun -deffnm md_0_1 -cpi -append

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From myunggi at pukyong.ac.kr  Fri Jan 17 02:03:02 2020
From: myunggi at pukyong.ac.kr (Myunggi Yi)
Date: Fri, 17 Jan 2020 01:03:02 -0000
Subject: [gmx-users] Hydrogen bonding criteria in Gromacs
In-Reply-To: <eab5575d-29f2-b427-49dd-ffa8607465aa@vt.edu>
References: <DB6PR0101MB2424708E45DFBC1D054F3E52EB370@DB6PR0101MB2424.eurprd01.prod.exchangelabs.com>
	<e846b411-71ae-1a7a-2936-7ed5f757fdc7@vt.edu>
	<CAHXfRVNQ0Kg-8LqqtSFkx0kjYB=gB7x2o8v0N1q_KnSLkHCZ2Q@mail.gmail.com>
	<eab5575d-29f2-b427-49dd-ffa8607465aa@vt.edu>
Message-ID: <CAHXfRVNX+oW0yXvBiZZPKa1KnWqrHYw1GQ_kfQsLd0c2w_s0Nw@mail.gmail.com>

Dear users,

If H-D-A angle is 30 degrees (for a case D-H distance is 1.0 A and D-A
distance is 3.3 A)
then the angle D-H-A is 138.3915 degrees.

D-A distance: 3.3 Angstroms and H-D-A angle: 30 degrees
are generous criteria to identify most hydrogen bonds.

It seems many people use them too.



On Thu, Jan 16, 2020 at 8:20 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/15/20 10:05 PM, Myunggi Yi wrote:
> > Dear Dr. Justin Lemkul,
> >
> > Can you explain why the D-H-A is 150?
> >
> > If H-D-A is 30, then D-H-A should be smaller than 150 degrees.
> > Since the sum of interior angles of a triangle should be 180 degrees...
> > See the following triangle.
> >
> >                       H
> >
> > D                                                           A
> >
> >
> > Am I missing something?
> >
>
> It's a deviation from linearity. An ideal hydrogen bond has a D-H-A
> angle of 180, thus H-D-A of 0. So the 30 degree values specified in
> GROMACS is effectively the deviation from linearity rather than being
> the complement of this value, which other software uses.
>
> -Justin
>
> > On Thu, Jan 16, 2020 at 2:30 AM Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >> On 1/15/20 11:57 AM, Pandya, Akash wrote:
> >>> Hi all,
> >>>
> >>> I  wanted to ask a couple of questions about the hydrogen bonding
> >> calculation in Gromacs.
> >>>
> >>>     1.   Why is the default angle cutoff 30 degrees? The reason I ask
> >> this is because I?ve seen in other packages with higher angle cutoffs.
> >>
> >> It depends on how the software defines the angle. The GROMACS convention
> >> is the angle corresponds to H-D-A rather than D-H-A like some other
> >> programs. H-D-A cutoff of 30 degrees is equivalent to the "conventional"
> >> 150-degree D-H-A cutoff.
> >>
> >>>     2.  What?s the best way to define cutoffs for my system? I know
> this
> >> is ambiguous, but is there a procedure I can use to decide?
> >>
> >> The default criteria are widely used and usually don't require any
> tuning.
> >>
> >> -Justin
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Office: 301 Fralin Hall
> >> Lab: 303 Engel Hall
> >>
> >> Virginia Tech Department of Biochemistry
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalemkul at vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==================================================
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

From bhupendra.dandekar001 at gmail.com  Fri Jan 17 04:23:36 2020
From: bhupendra.dandekar001 at gmail.com (Bhupendra Dandekar)
Date: Fri, 17 Jan 2020 03:23:36 -0000
Subject: [gmx-users] Calculating C-alpha RMSD for coarse grained
	simulation
In-Reply-To: <CAB5hSouF5uyyFpA4C41s0nqsr96eEfZKh+kV-NRwz5r9Rc-XvA@mail.gmail.com>
References: <CAB5hSovBCzLgQb-kjBNMTyg_XszXGeSd3LximgnM5kXFitqJDg@mail.gmail.com>
	<CA+jgKGVdL3oXjW=jcsq-zx_TijpfBm26XcL7aYYyLKk7DBCRWg@mail.gmail.com>
	<CAB5hSouF5uyyFpA4C41s0nqsr96eEfZKh+kV-NRwz5r9Rc-XvA@mail.gmail.com>
Message-ID: <CA+jgKGU5hqb-wE2V1LfG5DWPnb_JGXwuknq_UC=s0sn=2AUf8w@mail.gmail.com>

You welcome. Also there is detail information on the pbc correction on
gromacs page, kindly see that.

Bhupendra

On Fri, Jan 17, 2020, 4:02 AM Rabeta Yeasmin <rabetayeasmin at gmail.com>
wrote:

> Hi,
>
> I have solved the issue. I had problem in pbc correction step. It is good
> to follow some steps in order to get a good result. What I have used is
> -First made the molecules as whole to remove stretching in the structures
> (protein, membrane) due to pbc effect.
> *gmx trjconv -s step6.0_minimization.tpr -f 0A-1.xtc -o 0A-1-pbc-whole.xtc
> -pbc whole -n index-all.ndx*
>
> But my protein is a dimer, this command made the two monomer separated.
> That's why I had to cluster the two monomer after the above command.
> *gmx trjconv -s step6.0_minimization.tpr -f 0A-1-pbc-whole.xtc -o
> 0A-1-pbc-whole-cluster.xtc -pbc cluster -n index-all-new.ndx*
>
> I had calculated the RMSD after this, it looks reasonable now.
> Thanks for suggesting to check the trajectory.
>
> Rabeta Yeasmin
>
> On Thu, Jan 16, 2020 at 10:46 AM Bhupendra Dandekar <
> bhupendra.dandekar001 at gmail.com> wrote:
>
>> I will look into this and get back to you again. But meanwhile just try
>> using .tpr file instead of.gro file in your pbc correction step.
>>
>> Thanks
>> Bhupendra
>>
>> On Thu, Jan 16, 2020, 10:07 PM Rabeta Yeasmin <rabetayeasmin at gmail.com>
>> wrote:
>>
>>> Hi Bhupendra,
>>>
>>> Thanks for your reply. The RMSD is actually 3.5nm means 35A, which seems
>>> very large compared to the RMSD of that protein in all-atom simulation
>>> which is mostly between 5-6A. I have checked the trajectory as you
>>> suggested, My system is a dimer protein inside a lipid bilayer and it looks
>>> like if I remove the pbc effect using the following command
>>> *gmx trjconv -s 0A.gro -f 0A-2.xtc -o 0A-2-pbc.xtc -pbc nojump -ur
>>> compact -n index-all.ndx*
>>>
>>> the protein structure get stretched all the time  which causes the RMSD
>>> to be so high all-the time. If I use the original trajectory, the RMSD is
>>> usually 0.9nm to 1.5nm except when the protein encounter pbc effect. I am
>>> wondering how can I remove pbc effect without stretching the protein and
>>> keeping the dimer as a whole.
>>>
>>> Thanks.
>>> Rabeta Yeasmin
>>>
>>>

From bhupendra.dandekar001 at gmail.com  Fri Jan 17 04:23:37 2020
From: bhupendra.dandekar001 at gmail.com (Bhupendra Dandekar)
Date: Fri, 17 Jan 2020 03:23:37 -0000
Subject: [gmx-users] Calculating C-alpha RMSD for coarse grained
	simulation
In-Reply-To: <CAB5hSouF5uyyFpA4C41s0nqsr96eEfZKh+kV-NRwz5r9Rc-XvA@mail.gmail.com>
References: <CAB5hSovBCzLgQb-kjBNMTyg_XszXGeSd3LximgnM5kXFitqJDg@mail.gmail.com>
	<CA+jgKGVdL3oXjW=jcsq-zx_TijpfBm26XcL7aYYyLKk7DBCRWg@mail.gmail.com>
	<CAB5hSouF5uyyFpA4C41s0nqsr96eEfZKh+kV-NRwz5r9Rc-XvA@mail.gmail.com>
Message-ID: <CA+jgKGU5hqb-wE2V1LfG5DWPnb_JGXwuknq_UC=s0sn=2AUf8w@mail.gmail.com>

You welcome. Also there is detail information on the pbc correction on
gromacs page, kindly see that.

Bhupendra

On Fri, Jan 17, 2020, 4:02 AM Rabeta Yeasmin <rabetayeasmin at gmail.com>
wrote:

> Hi,
>
> I have solved the issue. I had problem in pbc correction step. It is good
> to follow some steps in order to get a good result. What I have used is
> -First made the molecules as whole to remove stretching in the structures
> (protein, membrane) due to pbc effect.
> *gmx trjconv -s step6.0_minimization.tpr -f 0A-1.xtc -o 0A-1-pbc-whole.xtc
> -pbc whole -n index-all.ndx*
>
> But my protein is a dimer, this command made the two monomer separated.
> That's why I had to cluster the two monomer after the above command.
> *gmx trjconv -s step6.0_minimization.tpr -f 0A-1-pbc-whole.xtc -o
> 0A-1-pbc-whole-cluster.xtc -pbc cluster -n index-all-new.ndx*
>
> I had calculated the RMSD after this, it looks reasonable now.
> Thanks for suggesting to check the trajectory.
>
> Rabeta Yeasmin
>
> On Thu, Jan 16, 2020 at 10:46 AM Bhupendra Dandekar <
> bhupendra.dandekar001 at gmail.com> wrote:
>
>> I will look into this and get back to you again. But meanwhile just try
>> using .tpr file instead of.gro file in your pbc correction step.
>>
>> Thanks
>> Bhupendra
>>
>> On Thu, Jan 16, 2020, 10:07 PM Rabeta Yeasmin <rabetayeasmin at gmail.com>
>> wrote:
>>
>>> Hi Bhupendra,
>>>
>>> Thanks for your reply. The RMSD is actually 3.5nm means 35A, which seems
>>> very large compared to the RMSD of that protein in all-atom simulation
>>> which is mostly between 5-6A. I have checked the trajectory as you
>>> suggested, My system is a dimer protein inside a lipid bilayer and it looks
>>> like if I remove the pbc effect using the following command
>>> *gmx trjconv -s 0A.gro -f 0A-2.xtc -o 0A-2-pbc.xtc -pbc nojump -ur
>>> compact -n index-all.ndx*
>>>
>>> the protein structure get stretched all the time  which causes the RMSD
>>> to be so high all-the time. If I use the original trajectory, the RMSD is
>>> usually 0.9nm to 1.5nm except when the protein encounter pbc effect. I am
>>> wondering how can I remove pbc effect without stretching the protein and
>>> keeping the dimer as a whole.
>>>
>>> Thanks.
>>> Rabeta Yeasmin
>>>
>>>

From ashmakhan200 at gmail.com  Fri Jan 17 06:39:08 2020
From: ashmakhan200 at gmail.com (Ashma Khan)
Date: Fri, 17 Jan 2020 05:39:08 -0000
Subject: [gmx-users] Regarding high RMSD
Message-ID: <CAG89CR4QQF-UsZoHFw-kFgOUWSQUkQF2Pif=FJFJdpE17jkaaQ@mail.gmail.com>

Thank you for your suggestion Alessandra Villa
I have applied all types of pbc conditions but my one peptide is diffusing
away from another peptide in case of dimer after half of the simulation
time and rmsd is coming out 100 Angstrom after that time which is very
high. Please suggest me what should I do.
-- 
Ashma Khan
Research Scholar
Department of Chemistry
AMU, Aligarh

From subhadipbasu4 at gmail.com  Fri Jan 17 07:22:08 2020
From: subhadipbasu4 at gmail.com (Subhadip Basu)
Date: Fri, 17 Jan 2020 06:22:08 -0000
Subject: [gmx-users] Can I use gromacs order to compute tetrahedral order
	parameter of water?
Message-ID: <CAFi7+1TEL2RtFM1cbjPD45CwcEd6ykhMw7VU+gobefa5f3Q2oA@mail.gmail.com>

 Dear gromacs users,
I want to calculate Orientational tetrahedral order parameter of water. The
output of gmx_hydorder is confusing. can I use gmx_order instead?

Thanks,

Subhadip Basu
Ph.D Student
Materials Research Centre
Indian Institute of Science
Bangalore 12
Contact no. +918277396508

From muthubioinf at gmail.com  Fri Jan 17 08:23:17 2020
From: muthubioinf at gmail.com (Muthusankar)
Date: Fri, 17 Jan 2020 07:23:17 -0000
Subject: [gmx-users] cluster analysis_group selection
Message-ID: <CAAuB-_rXnJAMMrZ7J4EvR8NHsN=Oa1OqBGuA80czSDKpAdmL0w@mail.gmail.com>

Dear Gromacs Users,
I ran the MD simulation of Membrane environment of protein at 100ns. I
would like to analysis of clustering methods.
I am planning to generate 'rmsd-matrix.xpm' and run 'gmx cluster' job but i
don't know which group select both for cluster analysis. could you guide
me, how to run the command and analysis also.

Thanks.
*Muthu Sankar*
Email: muthubioinf at gmail.com
Mobile No.  +91 9080444540

From nirali.d.imsc14 at ahduni.edu.in  Fri Jan 17 08:32:35 2020
From: nirali.d.imsc14 at ahduni.edu.in (Nirali Desai)
Date: Fri, 17 Jan 2020 07:32:35 -0000
Subject: [gmx-users] Problem while running equilibration
Message-ID: <CAKrv=HbRN2xdB0O043gcD0DzJJ1=z257oyqMcwGsjycGYKPrzQ@mail.gmail.com>

Dear all,

My system consists of a three chains of protein: PROA, PROB and PROCLIG
(with ligand).
Minimization is running properly without any error.
Parameters used are:
title = Minimization ; Title of run
define          = -DPOSRES

; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000   ; Stop minimization when the maximum force < 10.0 kJ/mol
emstep      = 0.01      ; Energy step size
nsteps = 50000   ; Maximum number of (minimization) steps to perform
energygrps = PROA PROB PROCLIG SOL ; Which energy group(s) to write to disk
energygrp_excl  = PROA PROA PROB PROB PROCLIG PROCLIG SOL SOL PROA SOL PROB
SOL
freezegrps      = PROCLIG
freezedim       = Y Y Y

But, while running equilibration it is giving error of the blowing up of
the system like water molecule not settled, clashes etc.
I ran the equilibration without adding water and also without using freeze
groups. It is running perfectly. I turned off constraints and pressure
coupling while using freezegroups.
 Parameters used:

title       = Protein-ligand complex NVT equilibration
define      = -DPOSRES  ; position restrain the protein and ligand
; Run parameters
integrator  = md        ; leap-frog integrator
nsteps      = 50000     ; 2 * 50000 = 100 ps
dt          = 0.002     ; 2 fs
; Output control
nstxout     = 100       ; save coordinates every 0.2 ps
nstvout     = 100       ; save velocities every 0.2 ps
nstenergy   = 100       ; save energies every 0.2 ps
nstlog      = 100       ; update log file every 0.2 ps
energygrps = PROA PROB PROCLIG SOL ; Which energy group(s) to write to disk
energygrp_excl  = PROA PROA PROB PROB PROCLIG PROCLIG SOL SOL PROA SOL PROB
SOL
freezegrps      = PROCLIG
freezedim       = Y Y Y
; Bond parameters
continuation    = no            ; first dynamics run
constraints     = none     ; all bonds (even heavy atom-H bonds) constrained
; Neighborsearching
ns_type     = grid      ; search neighboring grid cells
cutoff-scheme  = group
nstlist     = 20         ; 10 fs
rlist       = 0.9       ; short-range neighborlist cutoff (in nm)
rcoulomb    = 0.9       ; short-range electrostatic cutoff (in nm)
rvdw        = 0.9       ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype     = PME       ; Particle Mesh Ewald for long-range
electrostatics
pme_order       = 4         ; cubic interpolation
fourierspacing  = 0.16      ; grid spacing for FFT
; Temperature coupling
tcoupl      = V-rescale                     ; modified Berendsen thermostat
tc-grps     = Protein non-protein   ; two coupling groups - more accurate
tau_t       = 0.1   0.1                     ; time constant, in ps
ref_t       = 300   300                     ; reference temperature, one
for each group, in K
; Pressure coupling
pcoupl      = no        ; no pressure coupling in NVT
; Periodic boundary conditions
pbc         = xyz       ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel     = yes       ; assign velocities from Maxwell distribution
gen_temp    = 300       ; temperature for Maxwell distribution
gen_seed    = -1        ; generate a random seed

Please guide me on this.
If you have any suggestions I will really appreciate.

Thanks and regards,
Nirali

From gmx3 at hotmail.com  Fri Jan 17 09:01:22 2020
From: gmx3 at hotmail.com (Berk Hess)
Date: Fri, 17 Jan 2020 08:01:22 -0000
Subject: [gmx-users] com motion and position restraints may
	cause	artifacts
In-Reply-To: <CAAHQ3w=RK5QuyAV733+nK0A3N09BGEnZPie=QH3tS+9tS+-6Nw@mail.gmail.com>
References: <CAAHQ3wkvyk9UmO_5=YYEVQLhtetEEVwqVXp-jyEY55DgW-sRqg@mail.gmail.com>
	<CANogp5wm2T7QDHG5wpw16PBqqXvBU=YKUckdAT5a4-k-+JMmyQ@mail.gmail.com>
	<d2752133-25de-0e26-1266-4c5f599e0122@vt.edu>,
	<CAAHQ3w=RK5QuyAV733+nK0A3N09BGEnZPie=QH3tS+9tS+-6Nw@mail.gmail.com>
Message-ID: <AM6PR0202MB3287636AF87434F50EFA69BF8E310@AM6PR0202MB3287.eurprd02.prod.outlook.com>

Hi,

Using center of mass motion removal in combination with an absolute reference in the system, such as position restraints, will always lead to artifacts, as physical motion is removed and not drift due to numerical rounding errors. For the most common case of equilibrating macromolecules using position restraints these artifacts are usually negligible.

So we should probably add a sentence to the note:
Removing center of mass motion in the presence of positions restraints  might cause artifacts. When position restraints are used to equilibrate a macromolecule these artifacts are usually negligible.

I think we should add a comm-removal setting "auto" which should be the default, so grompp can automatically turn off comm-removal when using position restraints.

I realize now that we should check if there are no other artifacts when doing equilibration with position restraints in an NPT ensemble without comm-removal. I expect NVT should be fine without comm-removal.

Cheers,

Berk

________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Christos Deligkaris <deligkaris at gmail.com>
Sent: Thursday, January 16, 2020 5:03 PM
To: gmx-users at gromacs.org <gmx-users at gromacs.org>
Subject: Re: [gmx-users] com motion and position restraints may cause artifacts

The ambiguity in the gromacs 2020 note made me concerned, as it was
not clear to me whether my system (DNA+small molecule) fills in the
category where artifacts are caused. The gromacs note could have been
a bit more helpful by referencing specific publications so that we can
educate ourselves.....

Best wishes,

Christos Deligkaris, PhD

On Thu, Jan 16, 2020 at 5:21 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> On 1/16/20 5:17 AM, Alessandra Villa wrote:
> > Hi,
> >
> > On Mon, Jan 13, 2020 at 3:36 PM Christos Deligkaris <deligkaris at gmail.com>
> > wrote:
> >
> >> dear all,
> >>
> >> I installed gromacs 2020 and I now get the following message during
> >> equilibration:
> >>
> >> NOTE 1 [file nvt.mdp]:
> >>
> >>    Removing center of mass motion in the presence of position
> >> restraints  might cause artifacts
> >>
> >> I do not recall seeing this with gromacs 2018. In which cases are
> >> artifacts created? Is it now recommended to not remove the center of
> >> mass motion during equilibration?
> >>
> >>
> > It is recommended not to have position restrain and remove of center of
> > mass at the same moment. That is also the case of the equilibration phase.
> > That may cause artifact depending on the system and the condition you are
> > simulating.
>
> What is the nature of these artifacts and where is this documented?
> Combining position restraints with COM motion removal is an extremely
> common practice. Phrases like "might cause artifacts" are troubling
> because that implies uncertainty. Are there cases when this combination
> does not cause artifacts?
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

From alessandra.villa.biosim at gmail.com  Fri Jan 17 09:33:32 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Fri, 17 Jan 2020 08:33:32 -0000
Subject: [gmx-users] Regarding high RMSD
In-Reply-To: <CAG89CR4QQF-UsZoHFw-kFgOUWSQUkQF2Pif=FJFJdpE17jkaaQ@mail.gmail.com>
References: <CAG89CR4QQF-UsZoHFw-kFgOUWSQUkQF2Pif=FJFJdpE17jkaaQ@mail.gmail.com>
Message-ID: <CANogp5wsdgUT3+kP+ktJXe5osGgaJXGHYe2rENMdSntv7PRzbw@mail.gmail.com>

Hi,

On Fri, Jan 17, 2020 at 6:39 AM Ashma Khan <ashmakhan200 at gmail.com> wrote:

> Thank you for your suggestion Alessandra Villa
> I have applied all types of pbc conditions but my one peptide is diffusing
> away from another peptide in case of dimer after half of the simulation
> time and rmsd is coming out 100 Angstrom after that time which is very
> high. Please suggest me what should I do.
>

When you visualize the trajectory (for example in VMD), you see the dimer
breaking and the two peptides moving apart inside the box
(in a "continuous" way and not jumping in and out the box or moving out of
the box).
That probably means that in your simulation condition, the two peptides do
not form a dimer.

Best regards
Alessandra





> --
> Ashma Khan
> Research Scholar
> Department of Chemistry
> AMU, Aligarh
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Fri Jan 17 09:33:32 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Fri, 17 Jan 2020 08:33:32 -0000
Subject: [gmx-users] Regarding high RMSD
In-Reply-To: <CAG89CR4QQF-UsZoHFw-kFgOUWSQUkQF2Pif=FJFJdpE17jkaaQ@mail.gmail.com>
References: <CAG89CR4QQF-UsZoHFw-kFgOUWSQUkQF2Pif=FJFJdpE17jkaaQ@mail.gmail.com>
Message-ID: <CANogp5wsdgUT3+kP+ktJXe5osGgaJXGHYe2rENMdSntv7PRzbw@mail.gmail.com>

Hi,

On Fri, Jan 17, 2020 at 6:39 AM Ashma Khan <ashmakhan200 at gmail.com> wrote:

> Thank you for your suggestion Alessandra Villa
> I have applied all types of pbc conditions but my one peptide is diffusing
> away from another peptide in case of dimer after half of the simulation
> time and rmsd is coming out 100 Angstrom after that time which is very
> high. Please suggest me what should I do.
>

When you visualize the trajectory (for example in VMD), you see the dimer
breaking and the two peptides moving apart inside the box
(in a "continuous" way and not jumping in and out the box or moving out of
the box).
That probably means that in your simulation condition, the two peptides do
not form a dimer.

Best regards
Alessandra





> --
> Ashma Khan
> Research Scholar
> Department of Chemistry
> AMU, Aligarh
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Fri Jan 17 09:57:27 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Fri, 17 Jan 2020 08:57:27 -0000
Subject: [gmx-users] Problem while running equilibration
In-Reply-To: <CAKrv=HbRN2xdB0O043gcD0DzJJ1=z257oyqMcwGsjycGYKPrzQ@mail.gmail.com>
References: <CAKrv=HbRN2xdB0O043gcD0DzJJ1=z257oyqMcwGsjycGYKPrzQ@mail.gmail.com>
Message-ID: <CANogp5wY8i38SLp-T+1OeWs0jVrAMxR00VFXG1Qr+94=1tsPEQ@mail.gmail.com>

Hi,
see some comments/suggestions below.
Best regards
Alessandra

On Fri, Jan 17, 2020 at 8:34 AM Nirali Desai <nirali.d.imsc14 at ahduni.edu.in>
wrote:

> Dear all,
>
> My system consists of a three chains of protein: PROA, PROB and PROCLIG
> (with ligand).
> Minimization is running properly without any error.
> Parameters used are:
> title = Minimization ; Title of run
> define          = -DPOSRES
>
> ; Parameters describing what to do, when to stop and what to save
> integrator = steep ; Algorithm (steep = steepest descent minimization)
> emtol = 1000   ; Stop minimization when the maximum force < 10.0 kJ/mol
> emstep      = 0.01      ; Energy step size
> nsteps = 50000   ; Maximum number of (minimization) steps to perform
> energygrps = PROA PROB PROCLIG SOL ; Which energy group(s) to write to disk
> energygrp_excl  = PROA PROA PROB PROB PROCLIG PROCLIG SOL SOL PROA SOL PROB
> SOL
> freezegrps      = PROCLIG
> freezedim       = Y Y Y
>
> But, while running equilibration it is giving error of the blowing up of
> the system like water molecule not settled, clashes etc.
> I ran the equilibration without adding water and also without using freeze
> groups. It is running perfectly. I turned off constraints and pressure
> coupling while using freezegroups.
>  Parameters used:
>
> title       = Protein-ligand complex NVT equilibration
> define      = -DPOSRES  ; position restrain the protein and ligand
>


> ; Run parameters
> integrator  = md        ; leap-frog integrator
> nsteps      = 50000     ; 2 * 50000 = 100 ps
> dt          = 0.002     ; 2 fs
> ; Output control
> nstxout     = 100       ; save coordinates every 0.2 ps
> nstvout     = 100       ; save velocities every 0.2 ps
> nstenergy   = 100       ; save energies every 0.2 ps
> nstlog      = 100       ; update log file every 0.2 ps
> energygrps = PROA PROB PROCLIG SOL ; Which energy group(s) to write to disk
> energygrp_excl  = PROA PROA PROB PROB PROCLIG PROCLIG SOL SOL PROA SOL PROB
> SOL
>

Why do you use energygrp_excl ?   Usually  energygrp_excl are useful for
speeding up energy calculations with mdrun -rerun and for excluding
interactions within frozen groups (in your case only PROCLIG)

freezegrps      = PROCLIG
> freezedim       = Y Y Y
>

Do you need to freeze group?
You already have position restrains on protein and ligand



> ; Bond parameters
> continuation    = no            ; first dynamics run
> constraints     = none     ; all bonds (even heavy atom-H bonds)
> constrained
>

You are using 2fs and atomistic force field, then you need at least h-bond
to be constrained



> ; Neighborsearching
> ns_type     = grid      ; search neighboring grid cells
> cutoff-scheme  = group
> nstlist     = 20         ; 10 fs
> rlist       = 0.9       ; short-range neighborlist cutoff (in nm)
> rcoulomb    = 0.9       ; short-range electrostatic cutoff (in nm)
> rvdw        = 0.9       ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype     = PME       ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order       = 4         ; cubic interpolation
> fourierspacing  = 0.16      ; grid spacing for FFT
> ; Temperature coupling
> tcoupl      = V-rescale                     ; modified Berendsen thermostat
> tc-grps     = Protein non-protein   ; two coupling groups - more accurate
> tau_t       = 0.1   0.1                     ; time constant, in ps
> ref_t       = 300   300                     ; reference temperature, one
> for each group, in K
> ; Pressure coupling
> pcoupl      = no        ; no pressure coupling in NVT
> ; Periodic boundary conditions
> pbc         = xyz       ; 3-D PBC
> ; Dispersion correction
> DispCorr    = EnerPres  ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel     = yes       ; assign velocities from Maxwell distribution
> gen_temp    = 300       ; temperature for Maxwell distribution
> gen_seed    = -1        ; generate a random seed
>
> Please guide me on this.
> If you have any suggestions I will really appreciate.
>
> Thanks and regards,
> Nirali
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Fri Jan 17 09:57:27 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Fri, 17 Jan 2020 08:57:27 -0000
Subject: [gmx-users] Problem while running equilibration
In-Reply-To: <CAKrv=HbRN2xdB0O043gcD0DzJJ1=z257oyqMcwGsjycGYKPrzQ@mail.gmail.com>
References: <CAKrv=HbRN2xdB0O043gcD0DzJJ1=z257oyqMcwGsjycGYKPrzQ@mail.gmail.com>
Message-ID: <CANogp5wY8i38SLp-T+1OeWs0jVrAMxR00VFXG1Qr+94=1tsPEQ@mail.gmail.com>

Hi,
see some comments/suggestions below.
Best regards
Alessandra

On Fri, Jan 17, 2020 at 8:34 AM Nirali Desai <nirali.d.imsc14 at ahduni.edu.in>
wrote:

> Dear all,
>
> My system consists of a three chains of protein: PROA, PROB and PROCLIG
> (with ligand).
> Minimization is running properly without any error.
> Parameters used are:
> title = Minimization ; Title of run
> define          = -DPOSRES
>
> ; Parameters describing what to do, when to stop and what to save
> integrator = steep ; Algorithm (steep = steepest descent minimization)
> emtol = 1000   ; Stop minimization when the maximum force < 10.0 kJ/mol
> emstep      = 0.01      ; Energy step size
> nsteps = 50000   ; Maximum number of (minimization) steps to perform
> energygrps = PROA PROB PROCLIG SOL ; Which energy group(s) to write to disk
> energygrp_excl  = PROA PROA PROB PROB PROCLIG PROCLIG SOL SOL PROA SOL PROB
> SOL
> freezegrps      = PROCLIG
> freezedim       = Y Y Y
>
> But, while running equilibration it is giving error of the blowing up of
> the system like water molecule not settled, clashes etc.
> I ran the equilibration without adding water and also without using freeze
> groups. It is running perfectly. I turned off constraints and pressure
> coupling while using freezegroups.
>  Parameters used:
>
> title       = Protein-ligand complex NVT equilibration
> define      = -DPOSRES  ; position restrain the protein and ligand
>


> ; Run parameters
> integrator  = md        ; leap-frog integrator
> nsteps      = 50000     ; 2 * 50000 = 100 ps
> dt          = 0.002     ; 2 fs
> ; Output control
> nstxout     = 100       ; save coordinates every 0.2 ps
> nstvout     = 100       ; save velocities every 0.2 ps
> nstenergy   = 100       ; save energies every 0.2 ps
> nstlog      = 100       ; update log file every 0.2 ps
> energygrps = PROA PROB PROCLIG SOL ; Which energy group(s) to write to disk
> energygrp_excl  = PROA PROA PROB PROB PROCLIG PROCLIG SOL SOL PROA SOL PROB
> SOL
>

Why do you use energygrp_excl ?   Usually  energygrp_excl are useful for
speeding up energy calculations with mdrun -rerun and for excluding
interactions within frozen groups (in your case only PROCLIG)

freezegrps      = PROCLIG
> freezedim       = Y Y Y
>

Do you need to freeze group?
You already have position restrains on protein and ligand



> ; Bond parameters
> continuation    = no            ; first dynamics run
> constraints     = none     ; all bonds (even heavy atom-H bonds)
> constrained
>

You are using 2fs and atomistic force field, then you need at least h-bond
to be constrained



> ; Neighborsearching
> ns_type     = grid      ; search neighboring grid cells
> cutoff-scheme  = group
> nstlist     = 20         ; 10 fs
> rlist       = 0.9       ; short-range neighborlist cutoff (in nm)
> rcoulomb    = 0.9       ; short-range electrostatic cutoff (in nm)
> rvdw        = 0.9       ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype     = PME       ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order       = 4         ; cubic interpolation
> fourierspacing  = 0.16      ; grid spacing for FFT
> ; Temperature coupling
> tcoupl      = V-rescale                     ; modified Berendsen thermostat
> tc-grps     = Protein non-protein   ; two coupling groups - more accurate
> tau_t       = 0.1   0.1                     ; time constant, in ps
> ref_t       = 300   300                     ; reference temperature, one
> for each group, in K
> ; Pressure coupling
> pcoupl      = no        ; no pressure coupling in NVT
> ; Periodic boundary conditions
> pbc         = xyz       ; 3-D PBC
> ; Dispersion correction
> DispCorr    = EnerPres  ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel     = yes       ; assign velocities from Maxwell distribution
> gen_temp    = 300       ; temperature for Maxwell distribution
> gen_seed    = -1        ; generate a random seed
>
> Please guide me on this.
> If you have any suggestions I will really appreciate.
>
> Thanks and regards,
> Nirali
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From jin.jean.zhang at gmail.com  Fri Jan 17 10:10:25 2020
From: jin.jean.zhang at gmail.com (Jin Zhang)
Date: Fri, 17 Jan 2020 09:10:25 -0000
Subject: [gmx-users] cluster analysis_group selection
Message-ID: <CAGKd4OV2zhoCkY5ZbV+XiTsCe69_DSz4k=JuWAQLOqVDeyfpmA@mail.gmail.com>

Hi,

Hope this helps:
https://ctlee.github.io/BioChemCoRe-2018/clustering/
In case you may want to align the trajectory using one group but calculate
RMSD using another group, you can choose no fit when doing clustering. In
that case, gmx trajconv can be used before doing clustering.

Best,
Jin

From wacha.andras at ttk.hu  Fri Jan 17 10:33:43 2020
From: wacha.andras at ttk.hu (=?UTF-8?Q?Andr=c3=a1s_Ferenc_WACHA?=)
Date: Fri, 17 Jan 2020 09:33:43 -0000
Subject: [gmx-users] pdb2gmx picks up the wrong .tdb files?
In-Reply-To: <88435514-06b1-c1ce-fadf-757d583a39c3@vt.edu>
References: <bb2d0e87-595d-f6e5-d471-8c8e031168e7@ttk.hu>
	<3fa389b9-ec22-aa09-d112-05cdef3e09aa@vt.edu>
	<1224743b-d210-7c8c-4855-a22efbb336c0@ttk.hu>
	<e10a55fa-d20a-c779-e1c1-834044379c49@vt.edu>
	<4f683b2f-0fad-c0cc-92f0-a45a2d91e784@ttk.hu>
	<88435514-06b1-c1ce-fadf-757d583a39c3@vt.edu>
Message-ID: <061e16c0-3e9d-b59b-9c9f-2b3b556bcf16@ttk.hu>

Dear Justin,

there are no name clashes in the .rtp files by design, I never re-use
already existing residue names. Beta3-homo-lysine is B3K,
beta2-homo-lysine is B2K, and disubstituted amino-acids also have their
naming scheme.

Andras

On 1/16/20 11:34 PM, Justin Lemkul wrote:
>
>
> On 1/16/20 10:07 AM, Andr?s Ferenc WACHA wrote:
>>
>> Dear Justin,
>>
>> thank you. Am I doing something wrong or is this a bug in Gromacs? Do
>> you have a suggestion how to make this work? Should I rename the
>> terminal patches or should I put everything under one basename
>> (sacrificing cleanliness and maintainability)?
>>
>
> Without spending a long time going through the code, likely what is
> happening is pdb2gmx is loading the .rtp files in alphabetical order,
> finding the first match of LYS (which occurs in your beta-amino acid
> file) and loads the matching .tdb file - this is why alpha-amino acids
> don't work; they're interpreted as beta. The cleanest solution would
> probably be to prefix your beta-amino acids to change their residue
> names, e.g. BLYS instead of LYS in both the .rtp and coordinate files.
>
> -Justin
>
-- 
Andr?s Ferenc Wacha, PhD
research fellow, CREDO instrument responsible

Biological Nanochemistry Research Group (310)

Institute of Materials and Environmental Chemistry
Research Centre for Natural Sciences (RCNS)
Magyar tud?sok k?r?tja 2.
H-1117 Budapest, Hungary
Phone: +36-1-382-6427
Web: http://bionano.ttk.hu
CREDO SAXS instrument: http://credo.ttk.hu


-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 554 bytes
Desc: OpenPGP digital signature
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20200117/368eeb88/attachment-0001.sig>

From marko at kth.se  Fri Jan 17 11:54:30 2020
From: marko at kth.se (Marko Petrovic)
Date: Fri, 17 Jan 2020 10:54:30 -0000
Subject: [gmx-users] Ran into trouble installing Gromacs API
Message-ID: <5F39287A-B2D6-49EF-8585-B5F761275F85@kth.se>

Hello

I have (I think successfully) installed Gromacs 2020 on my computer (MacOS X Catalina) and tried to install the API using the quick install guide: https://gmxapi.readthedocs.io/en/latest/quickstart.html
and get stuck on the step:

pip install -r requirements.txt

as that file does not seem to be in that folder of the repo. I found the file "requirements-test.txt" in the folder "python-packaging" and tried with that but got a long error message of missing stuff I didn't understand, I'm hoping those error messages are from the file not being intended for use inn the manner I tried so I'm currently not including those here.

Should I have installed gromacs 2019 for which the API was developed? Has anyone else installed the API recently and (hopefully) exxperienced and overcome this hurdle?

With Regards
Marko Petrovic
Educator
Computational Science and Technology
School of Electrical Engineering and Computer Science
KTH Royal Institute of Technology


From vuqv.phys at gmail.com  Fri Jan 17 12:49:20 2020
From: vuqv.phys at gmail.com (Quyen V. Vu)
Date: Fri, 17 Jan 2020 11:49:20 -0000
Subject: [gmx-users] Why it is run so slow in gromacs 2019.3 compared to
 VERSION 5.1.1?
In-Reply-To: <b85b07f3-4111-28a5-4ac7-841fe87bb41e@vt.edu>
References: <tencent_B72778E0898ACC0EDEE547065FCEEEA11706@qq.com>
	<tencent_272F50F0AE937B99023CA48F383E81DD3607@qq.com>
	<tencent_8681571D38D249914C381EC987155FE2AE06@qq.com>
	<b85b07f3-4111-28a5-4ac7-841fe87bb41e@vt.edu>
Message-ID: <CA+CKAfz=Q4XtwoWLe_GUQV-C-F8Os9PZOUnCoQ85mAPd3ti8WQ@mail.gmail.com>

He said he ran a nearly identical simulation on two versions of gromacs but
I didn't think so,
in 2019.3 logs:

There are: 117860 Atoms
Atom distribution over 27 domains: av 4365 stddev 75 min 4289 max 4626
and 5.1 logs:
There are: 127790 Atoms
Atom distribution over 30 domains: av 4259 stddev 90 min 4193 max 4370

On Thu, Jan 16, 2020 at 11:37 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/16/20 11:57 AM, ZHANG Cheng wrote:
> > I have re-run the MD, with only 2 ps in both version. Indeed, the
> Version 2019 is far slower than the Version 5.1.1.
> >
> >
> > Version 2019 needs 114.111 hours to complete 1 ns, while Version 5.1.1
> only needs&nbsp;6.362 hours to complete 1 ns.&nbsp;
> >
> >
> > The new logs files are at
> > https://github.com/lanselibai/gromacs-20200116
> >
> >
> >
> > The MD is run on our HPC cluster. So I personally could not compile it.
> Is there still some way to get equivalent performance for the Version 2019?
> >
>
> Try assigning the same number of PP and PME ranks in each run (30/6 in
> 5.1.1 and 27/9 in 2019.3). You're losing a lot of performance in
> communicating PME forces in the 2019.3 run. You may also want to try
> version 2020 to see if automatic detection has improved.
>
> -Justin
>
> >
> >
> > ------------------&nbsp;Original&nbsp;------------------
> > From:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
> > Date:&nbsp;Thu, Jan 16, 2020 07:58 AM
> > To:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;"gromacs.org_gmx-users"<
> gromacs.org_gmx-users at maillist.sys.kth.se&gt;;
> >
> > Subject:&nbsp;Re:Why it is run so slow in gromacs 2019.3 compared to
> VERSION 5.1.1?
> >
> >
> >
> > Hi Justin, what kind of information should I look at in the log files?
> They are too big to paste here. Would it be possible if you can see them at
> https://github.com/lanselibai/gromacs-20200115&nbsp;?
> >
> >
> > Thank you!
> >
> >
> > ------------------ Original ------------------
> > From:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
> > Date:&nbsp;Thu, Jan 16, 2020 03:38 AM
> > To:&nbsp;"gromacs.org_gmx-users"<
> gromacs.org_gmx-users at maillist.sys.kth.se&gt;;
> > Cc:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
> > Subject:&nbsp;Why it is run so slow in gromacs 2019.3 compared to
> VERSION 5.1.1?
> >
> >
> >
> > I have a nearly identical run using the "VERSION 2019.3" compared to my
> previous "VERSION 5.1.1". Everything during the preparation is the same
> except "-r" needs to be added in the "VERSION 2019.3". So "-r em.gro", "-r
> nvt.gro" and "-r npt.gro" are added in the grompp commands for NVT, NPT and
> production run, respectively.
> >
> >
> > Using "-pe mpi 12" (i.e. 12 nodes) per hour, only 5-7 ps can be
> processed in the "VERSION 2019.3", while 200 ps can be achieved in the
> "VERSION 5.1.1". Can I ask is this normal? Is there some configuration I
> can do in the "VERSION 2019.3" so as to accelerate the MD?
> >
> >
> > I follow Justin's tutorial at
> http://www.mdtutorials.com/gmx/lysozyme/index.html
> > The commands I used are listed below.
> >
> >
> > gmx pdb2gmx&nbsp; -f Fab.pdb -o Fab_processed.gro -water spce&nbsp;
> -inter&nbsp; -ignh -merge interactive
> > gmx editconf -f Fab_processed.gro -o Fab_newbox.gro -c -d 1.0 -bt cubic
> > gmx solvate -cp Fab_newbox.gro -cs spc216.gro -o Fab_solv.gro -p
> topol.top
> > gmx grompp -f ions.mdp -c Fab_solv.gro -p topol.top -o ions.tpr -maxwarn
> 1
> > gmx genion -s ions.tpr -o Fab_solv_ions.gro -p topol.top -pname NA
> -nname CL -nn 31 -neutral -conc 0.05
> > (Afterwards, using the HPC to run)
> > gmx grompp -f minim.mdp -c Fab_solv_ions.gro -p topol.top -o em.tpr
> > gerun mdrun_mpi -v -deffnm em
> > gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -r em.gro
> > gerun mdrun_mpi -deffnm nvt
> > gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -r
> nvt.gro
> > gerun mdrun_mpi -deffnm npt
> > gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -r
> npt.gro
> > gmx mdrun -deffnm md_0_1 -cpi -append
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From 272699575 at qq.com  Fri Jan 17 13:12:43 2020
From: 272699575 at qq.com (=?ISO-8859-1?B?WkhBTkcgQ2hlbmc=?=)
Date: Fri, 17 Jan 2020 12:12:43 -0000
Subject: [gmx-users] Why it is run so slow in gromacs 2019.3 compared to
	VERSION 5.1.1?
In-Reply-To: <tencent_8681571D38D249914C381EC987155FE2AE06@qq.com>
References: <tencent_B72778E0898ACC0EDEE547065FCEEEA11706@qq.com>
	<tencent_272F50F0AE937B99023CA48F383E81DD3607@qq.com>
	<tencent_8681571D38D249914C381EC987155FE2AE06@qq.com>
Message-ID: <tencent_DFE5039A2F6B97C0EB0B1CEAC442860AAF05@qq.com>

Many thanks for Justin's advice for&nbsp;assigning the same number of PP and PME ranks in each run (30/6 in 5.1.1 and 27/9 in 2019.3). Sorry I am not familiar with these kind of settings, can I ask how to do this exactly? e.g. how to change "gmx mdrun -deffnm md_0_1 -cpi -append" ?




------------------&nbsp;Original&nbsp;------------------
From:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
Date:&nbsp;Fri, Jan 17, 2020 00:57 AM
To:&nbsp;"gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se&gt;;

Subject:&nbsp;Re:Re:Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?



I have re-run the MD, with only 2 ps in both version. Indeed, the Version 2019 is far slower than the Version 5.1.1.


Version 2019 needs 114.111 hours to complete 1 ns, while Version 5.1.1 only needs 6.362 hours to complete 1 ns. 


The new logs files are at
https://github.com/lanselibai/gromacs-20200116



The MD is run on our HPC cluster. So I personally could not compile it. Is there still some way to get equivalent performance for the Version 2019?




------------------ Original ------------------
From:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
Date:&nbsp;Thu, Jan 16, 2020 07:58 AM
To:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;"gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se&gt;;

Subject:&nbsp;Re:Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?



Hi Justin, what kind of information should I look at in the log files? They are too big to paste here. Would it be possible if you can see them at https://github.com/lanselibai/gromacs-20200115&nbsp;?


Thank you!


------------------ Original ------------------
From:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
Date:&nbsp;Thu, Jan 16, 2020 03:38 AM
To:&nbsp;"gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se&gt;;
Cc:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
Subject:&nbsp;Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?



I have a nearly identical run using the "VERSION 2019.3" compared to my previous "VERSION 5.1.1". Everything during the preparation is the same except "-r" needs to be added in the "VERSION 2019.3". So "-r em.gro", "-r nvt.gro" and "-r npt.gro" are added in the grompp commands for NVT, NPT and production run, respectively.


Using "-pe mpi 12" (i.e. 12 nodes) per hour, only 5-7 ps can be processed in the "VERSION 2019.3", while 200 ps can be achieved in the "VERSION 5.1.1". Can I ask is this normal? Is there some configuration I can do in the "VERSION 2019.3" so as to accelerate the MD? 


I follow Justin's tutorial at http://www.mdtutorials.com/gmx/lysozyme/index.html
The commands I used are listed below.


gmx pdb2gmx&nbsp; -f Fab.pdb -o Fab_processed.gro -water spce&nbsp; -inter&nbsp; -ignh -merge interactive
gmx editconf -f Fab_processed.gro -o Fab_newbox.gro -c -d 1.0 -bt cubic
gmx solvate -cp Fab_newbox.gro -cs spc216.gro -o Fab_solv.gro -p topol.top
gmx grompp -f ions.mdp -c Fab_solv.gro -p topol.top -o ions.tpr -maxwarn 1 
gmx genion -s ions.tpr -o Fab_solv_ions.gro -p topol.top -pname NA -nname CL -nn 31 -neutral -conc 0.05
(Afterwards, using the HPC to run)
gmx grompp -f minim.mdp -c Fab_solv_ions.gro -p topol.top -o em.tpr
gerun mdrun_mpi -v -deffnm em
gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -r em.gro
gerun mdrun_mpi -deffnm nvt
gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -r nvt.gro
gerun mdrun_mpi -deffnm npt
gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -r npt.gro
gmx mdrun -deffnm md_0_1 -cpi -append

From jalemkul at vt.edu  Fri Jan 17 14:19:12 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Fri, 17 Jan 2020 13:19:12 -0000
Subject: [gmx-users] Why it is run so slow in gromacs 2019.3 compared to
 VERSION 5.1.1?
In-Reply-To: <tencent_DFE5039A2F6B97C0EB0B1CEAC442860AAF05@qq.com>
References: <tencent_B72778E0898ACC0EDEE547065FCEEEA11706@qq.com>
	<tencent_272F50F0AE937B99023CA48F383E81DD3607@qq.com>
	<tencent_8681571D38D249914C381EC987155FE2AE06@qq.com>
	<tencent_DFE5039A2F6B97C0EB0B1CEAC442860AAF05@qq.com>
Message-ID: <3e3a3a3d-d55f-13ac-b350-269e1ed7ec89@vt.edu>



On 1/17/20 7:12 AM, ZHANG Cheng wrote:
> Many thanks for Justin's advice for&nbsp;assigning the same number of PP and PME ranks in each run (30/6 in 5.1.1 and 27/9 in 2019.3). Sorry I am not familiar with these kind of settings, can I ask how to do this exactly? e.g. how to change "gmx mdrun -deffnm md_0_1 -cpi -append" ?
>

As Quyen noted, you're simulating different systems with each version. 
You can't do that and expect to establish a benchmark. Run the exact 
same input in both versions to establish how well each performs.

If you want to tweak performance settings, refer to the manual and 
consult gmx help mdrun.

-Justin

>
>
> ------------------&nbsp;Original&nbsp;------------------
> From:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
> Date:&nbsp;Fri, Jan 17, 2020 00:57 AM
> To:&nbsp;"gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se&gt;;
>
> Subject:&nbsp;Re:Re:Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?
>
>
>
> I have re-run the MD, with only 2 ps in both version. Indeed, the Version 2019 is far slower than the Version 5.1.1.
>
>
> Version 2019 needs 114.111 hours to complete 1 ns, while Version 5.1.1 only needs 6.362 hours to complete 1 ns.
>
>
> The new logs files are at
> https://github.com/lanselibai/gromacs-20200116
>
>
>
> The MD is run on our HPC cluster. So I personally could not compile it. Is there still some way to get equivalent performance for the Version 2019?
>
>
>
>
> ------------------ Original ------------------
> From:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
> Date:&nbsp;Thu, Jan 16, 2020 07:58 AM
> To:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;"gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se&gt;;
>
> Subject:&nbsp;Re:Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?
>
>
>
> Hi Justin, what kind of information should I look at in the log files? They are too big to paste here. Would it be possible if you can see them at https://github.com/lanselibai/gromacs-20200115&nbsp;?
>
>
> Thank you!
>
>
> ------------------ Original ------------------
> From:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
> Date:&nbsp;Thu, Jan 16, 2020 03:38 AM
> To:&nbsp;"gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se&gt;;
> Cc:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
> Subject:&nbsp;Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?
>
>
>
> I have a nearly identical run using the "VERSION 2019.3" compared to my previous "VERSION 5.1.1". Everything during the preparation is the same except "-r" needs to be added in the "VERSION 2019.3". So "-r em.gro", "-r nvt.gro" and "-r npt.gro" are added in the grompp commands for NVT, NPT and production run, respectively.
>
>
> Using "-pe mpi 12" (i.e. 12 nodes) per hour, only 5-7 ps can be processed in the "VERSION 2019.3", while 200 ps can be achieved in the "VERSION 5.1.1". Can I ask is this normal? Is there some configuration I can do in the "VERSION 2019.3" so as to accelerate the MD?
>
>
> I follow Justin's tutorial at http://www.mdtutorials.com/gmx/lysozyme/index.html
> The commands I used are listed below.
>
>
> gmx pdb2gmx&nbsp; -f Fab.pdb -o Fab_processed.gro -water spce&nbsp; -inter&nbsp; -ignh -merge interactive
> gmx editconf -f Fab_processed.gro -o Fab_newbox.gro -c -d 1.0 -bt cubic
> gmx solvate -cp Fab_newbox.gro -cs spc216.gro -o Fab_solv.gro -p topol.top
> gmx grompp -f ions.mdp -c Fab_solv.gro -p topol.top -o ions.tpr -maxwarn 1
> gmx genion -s ions.tpr -o Fab_solv_ions.gro -p topol.top -pname NA -nname CL -nn 31 -neutral -conc 0.05
> (Afterwards, using the HPC to run)
> gmx grompp -f minim.mdp -c Fab_solv_ions.gro -p topol.top -o em.tpr
> gerun mdrun_mpi -v -deffnm em
> gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -r em.gro
> gerun mdrun_mpi -deffnm nvt
> gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -r nvt.gro
> gerun mdrun_mpi -deffnm npt
> gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -r npt.gro
> gmx mdrun -deffnm md_0_1 -cpi -append

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From jalemkul at vt.edu  Fri Jan 17 14:20:09 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Fri, 17 Jan 2020 13:20:09 -0000
Subject: [gmx-users] pdb2gmx picks up the wrong .tdb files?
In-Reply-To: <061e16c0-3e9d-b59b-9c9f-2b3b556bcf16@ttk.hu>
References: <bb2d0e87-595d-f6e5-d471-8c8e031168e7@ttk.hu>
	<3fa389b9-ec22-aa09-d112-05cdef3e09aa@vt.edu>
	<1224743b-d210-7c8c-4855-a22efbb336c0@ttk.hu>
	<e10a55fa-d20a-c779-e1c1-834044379c49@vt.edu>
	<4f683b2f-0fad-c0cc-92f0-a45a2d91e784@ttk.hu>
	<88435514-06b1-c1ce-fadf-757d583a39c3@vt.edu>
	<061e16c0-3e9d-b59b-9c9f-2b3b556bcf16@ttk.hu>
Message-ID: <90b7275e-cef5-518d-f7d3-aad14432c51b@vt.edu>



On 1/17/20 4:25 AM, Andr?s Ferenc WACHA wrote:
> Dear Justin,
>
> there are no name clashes in the .rtp files by design, I never re-use
> already existing residue names. Beta3-homo-lysine is B3K,
> beta2-homo-lysine is B2K, and disubstituted amino-acids also have their
> naming scheme.

Sorry, no idea. This should work out of the box, because it's the normal 
behavior in force fields that have e.g. aminoacids.rtp, dna.rtp, etc. 
with matching .tdb files. Without access to the force field to dig into 
it, there's not much I can suggest other than putting everything into 
merged.rtp, merged.*.tdb, etc.

-Justin

> Andras
>
> On 1/16/20 11:34 PM, Justin Lemkul wrote:
>>
>> On 1/16/20 10:07 AM, Andr?s Ferenc WACHA wrote:
>>> Dear Justin,
>>>
>>> thank you. Am I doing something wrong or is this a bug in Gromacs? Do
>>> you have a suggestion how to make this work? Should I rename the
>>> terminal patches or should I put everything under one basename
>>> (sacrificing cleanliness and maintainability)?
>>>
>> Without spending a long time going through the code, likely what is
>> happening is pdb2gmx is loading the .rtp files in alphabetical order,
>> finding the first match of LYS (which occurs in your beta-amino acid
>> file) and loads the matching .tdb file - this is why alpha-amino acids
>> don't work; they're interpreted as beta. The cleanest solution would
>> probably be to prefix your beta-amino acids to change their residue
>> names, e.g. BLYS instead of LYS in both the .rtp and coordinate files.
>>
>> -Justin
>>
>>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From jalemkul at vt.edu  Fri Jan 17 14:21:08 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Fri, 17 Jan 2020 13:21:08 -0000
Subject: [gmx-users] com motion and position restraints may cause
 artifacts
In-Reply-To: <AM6PR0202MB3287636AF87434F50EFA69BF8E310@AM6PR0202MB3287.eurprd02.prod.outlook.com>
References: <CAAHQ3wkvyk9UmO_5=YYEVQLhtetEEVwqVXp-jyEY55DgW-sRqg@mail.gmail.com>
	<CANogp5wm2T7QDHG5wpw16PBqqXvBU=YKUckdAT5a4-k-+JMmyQ@mail.gmail.com>
	<d2752133-25de-0e26-1266-4c5f599e0122@vt.edu>
	<CAAHQ3w=RK5QuyAV733+nK0A3N09BGEnZPie=QH3tS+9tS+-6Nw@mail.gmail.com>
	<AM6PR0202MB3287636AF87434F50EFA69BF8E310@AM6PR0202MB3287.eurprd02.prod.outlook.com>
Message-ID: <5d0df429-83cd-59c0-fe03-010734d2da46@vt.edu>



On 1/17/20 3:01 AM, Berk Hess wrote:
> Hi,
>
> Using center of mass motion removal in combination with an absolute reference in the system, such as position restraints, will always lead to artifacts, as physical motion is removed and not drift due to numerical rounding errors. For the most common case of equilibrating macromolecules using position restraints these artifacts are usually negligible.
>
> So we should probably add a sentence to the note:
> Removing center of mass motion in the presence of positions restraints  might cause artifacts. When position restraints are used to equilibrate a macromolecule these artifacts are usually negligible.

Thanks, Berk. I do think this addition would be important. Most people 
are going to encounter the note doing exactly what you describe, 
equilibrating a macromolecule. If the artifacts are negligible in this 
case, it should be made clear to avoid concern.

-Justin

> I think we should add a comm-removal setting "auto" which should be the default, so grompp can automatically turn off comm-removal when using position restraints.
>
> I realize now that we should check if there are no other artifacts when doing equilibration with position restraints in an NPT ensemble without comm-removal. I expect NVT should be fine without comm-removal.
>
> Cheers,
>
> Berk
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Christos Deligkaris <deligkaris at gmail.com>
> Sent: Thursday, January 16, 2020 5:03 PM
> To: gmx-users at gromacs.org <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] com motion and position restraints may cause artifacts
>
> The ambiguity in the gromacs 2020 note made me concerned, as it was
> not clear to me whether my system (DNA+small molecule) fills in the
> category where artifacts are caused. The gromacs note could have been
> a bit more helpful by referencing specific publications so that we can
> educate ourselves.....
>
> Best wishes,
>
> Christos Deligkaris, PhD
>
> On Thu, Jan 16, 2020 at 5:21 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>> On 1/16/20 5:17 AM, Alessandra Villa wrote:
>>> Hi,
>>>
>>> On Mon, Jan 13, 2020 at 3:36 PM Christos Deligkaris <deligkaris at gmail.com>
>>> wrote:
>>>
>>>> dear all,
>>>>
>>>> I installed gromacs 2020 and I now get the following message during
>>>> equilibration:
>>>>
>>>> NOTE 1 [file nvt.mdp]:
>>>>
>>>>     Removing center of mass motion in the presence of position
>>>> restraints  might cause artifacts
>>>>
>>>> I do not recall seeing this with gromacs 2018. In which cases are
>>>> artifacts created? Is it now recommended to not remove the center of
>>>> mass motion during equilibration?
>>>>
>>>>
>>> It is recommended not to have position restrain and remove of center of
>>> mass at the same moment. That is also the case of the equilibration phase.
>>> That may cause artifact depending on the system and the condition you are
>>> simulating.
>> What is the nature of these artifacts and where is this documented?
>> Combining position restraints with COM motion removal is an extremely
>> common practice. Phrases like "might cause artifacts" are troubling
>> because that implies uncertainty. Are there cases when this combination
>> does not cause artifacts?
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From bray at iupui.edu  Fri Jan 17 19:38:45 2020
From: bray at iupui.edu (Ray, Bruce D)
Date: Fri, 17 Jan 2020 18:38:45 -0000
Subject: [gmx-users] gmx_topolbuild error (aayattimg@bose.res.in)
In-Reply-To: <mailman.527.1578642997.1966.gromacs.org_gmx-users@maillist.sys.kth.se>
References: <mailman.527.1578642997.1966.gromacs.org_gmx-users@maillist.sys.kth.se>
Message-ID: <1579286124583.30046@iupui.edu>



On Fri, 10 Jan 2020 11:15:36 +0530 (IST) , aayattimg at bose.res.in<mailto:aayattimg at bose.res.in> wrote:

Date: Fri, 10 Jan 2020 11:15:36 +0530 (IST)
From: aayattimg at bose.res.in<mailto:aayattimg at bose.res.in>
To: gromacs.org_gmx-users at maillist.sys.kth.se<mailto:gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] gmx_topolbuild error
Message-ID: <48026.103.230.166.2.1578635136.squirrel at bose.res.in><mailto:48026.103.230.166.2.1578635136.squirrel at bose.res.in>
Content-Type: text/plain;charset=UTF-8

I am getting error in topolbuild:
Fatal error.
Source code file: readmol2.c, line: 693
Atom 1 (O5') has 2 connections when allowed 0
 I have used the command
./topolbuild -dir /home/aayatti/topolbuild1_2_1/dat/leap/parm -ff amber -n
tripos97
.mol2 file that I am using is as follows:
@<TRIPOS>MOLECULE
QCH
   30    31     1     0     1
SMALL
USER_CHARGES
@<TRIPOS>ATOM
  1 O5'        -1.938234    2.221639    0.669368 O         1 QCH
-0.6458 ****
  2 H5T        -2.161090    3.085515    0.989879 H         1 QCH
0.4497 ****
  3 O3'        -3.459429   -1.728789    0.016186 O         1 QCH
-0.6852 ****
  4 H3T        -3.700920   -2.323917    0.713748 H         1 QCH
0.4392 ****
  5 C1'        -0.662286   -0.787261   -0.296578 C         1 QCH
0.3964 ****
  6 H1'        -0.605691   -1.741658   -0.791073 H         1 QCH
0.0394 ****
  7 C2'        -1.435951   -0.850884    1.016075 C         1 QCH
-0.0947 ****
  8 H2'1       -1.108767   -0.064159    1.683744 H         1 QCH
0.0480 ****
  9 H2'2       -1.331556   -1.807305    1.511592 H         1 QCH
0.0480 ****
 10 C3'        -2.859368   -0.575997    0.536996 C         1 QCH
0.2991 ****
 11 H3'        -3.474441   -0.127033    1.307751 H         1 QCH
0.0153 ****
 12 C4'        -2.644620    0.372686   -0.650794 C         1 QCH
0.1743 ****
 13 H4'        -3.310149    0.087545   -1.452894 H         1 QCH
0.0890 ****
 14 C5'        -2.828924    1.845500   -0.355885 C         1 QCH
0.0150 ****
 15 H5'1       -2.633260    2.416008   -1.257986 H         1 QCH
0.0776 ****
 16 H5'2       -3.858755    2.018514   -0.059368 H         1 QCH
0.0776 ****
 17 O4'        -1.304632    0.148647   -1.085285 O         1 QCH
-0.4154 ****
 18 N1          0.746765   -0.330172   -0.139522 N         1 QCH
-0.0020 ****
 19 C6          1.037481    0.982281   -0.067547 C         1 QCH
-0.1180 ****
 20 H6          0.189023    1.636860   -0.090671 H         1 QCH
0.2766 ****
 21 C5          2.303418    1.459166    0.033557 C         1 QCH
-0.2943 ****
 22 H5          2.501789    2.509565    0.085307 H         1 QCH
0.1984 ****
 23 C4          3.355190    0.521532    0.053970 C         1 QCH
0.4864 ****
 24 N4          4.624825    0.860634    0.131082 N         1 QCH
-0.8725 ****
 25 H41         5.362632    0.189871    0.139293 H         1 QCH
0.4651 ****
 26 H42         4.887551    1.821377    0.170549 H         1 QCH
0.4651 ****
 27 N3          3.028239   -0.778715   -0.004253 N         1 QCH
-0.2232 ****
 28 H3          3.730821   -1.491229    0.018101 H         1 QCH
0.3215 ****
 29 C2          1.731998   -1.290150   -0.085103 C         1 QCH
0.4517 ****
 30 O2          1.543842   -2.458176   -0.098679 O         1 QCH
-0.4823 ****
@<TRIPOS>BOND
    1     1     2 1
    2     1    14 1
    3     3     4 1
    4     3    10 1
    5     5     6 1
    6     5     7 1
    7     5    17 1
    8     5    18 1
    9     7     8 1
   10     7     9 1
   11     7    10 1
   12    10    11 1
   13    10    12 1
   14    12    13 1
   15    12    14 1
   16    12    17 1
   17    14    15 1
   18    14    16 1
   19    18    19 1
   20    18    29 1
   21    19    20 1
   22    19    21 1
   23    21    22 1
   24    21    23 1
   25    23    24 1
   26    23    27 1
   27    24    25 1
   28    24    26 1
   29    27    28 1
   30    27    29 1
   31    29    30 1
@<TRIPOS>SUBSTRUCTURE
      1  QCH              1 ****               0 ****  ****




kindly suggest to debug the error.
Thanking you in advance.


You do not have a properly formatted *.mol2 file.  It lacks proper
Tripos atom types in the sixth column.  In topolbuild, correct Tripos
atom types are critical for assignment of atom types in the final
gromacs topology.  I am surprised that this error message was triggered
rather than a message about not being able to find the atom types.  When
I get time now that I have been forced into retirement in my old age, I
hope to get back to refining this program, always provided that I am
able to remember what I did almost a decade ago.  In the meantime,
your oxygens and carbons need proper Tripos atom topology types.

 --
Bruce David Ray


From travis.meyer at rutgers.edu  Fri Jan 17 20:29:00 2020
From: travis.meyer at rutgers.edu (Travis Meyer)
Date: Fri, 17 Jan 2020 19:29:00 -0000
Subject: [gmx-users] Troubleshooting Error Message: Invalid Index Group
	References
Message-ID: <BN8PR14MB317165831AA3007B03B76B5093310@BN8PR14MB3171.namprd14.prod.outlook.com>


    Thanks for your response! I checked and the cg_traj file contains atoms numbered 1-2000, which matches the atom IDs from the index file. The same trajectory does work using gmx angle with an angle index file created from the same python script which also includes atom IDs 1-2000 as well.
    The fact that the error says "largest allowed atom index is 0" seems especially interesting to me, as it implies the gmx distance isn't finding any atoms in the trajectory file.
    Travis Meyer, Ph.D.
    INSPIRE Postdoctoral Fellow
    Gormley Lab, Rutgers University
    > Hello all,
    >
    > I am a brand new MD/GROMACS user, and I have been trying to learn how to
    > use GROMACS for coarse-grained simulations using the MARTINI forcefield. I
    > was going through a tutorial on coarse-graining from the MARTINI website (
    > https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcgmartini.nl%2Findex.php%2Ftutorials-general-introduction-gmx5%2Fmartini-tutorials-polymers-gmx5&amp;data=02%7C01%7Ctravis.meyer%40rutgers.edu%7Cf110fee0c56e442a988308d79b7a1aee%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C637148821067442954&amp;sdata=rBs2IvNHERRNN5IQbflOJCGJezD4jVHWREeFC2%2FMTuY%3D&amp;reserved=0)
    > but ran into an error I have been not been able to find a solution for.
    >
    > After coarse-graining the all-atom simulation to the COM between 3 atoms,
    > I need to calculate bond lengths and angles in order to parameterize bonded
    > interactions. Following instructions from the tutorial, I created index
    > files for all bonds, angles, and dihedrals and used gmx distance along with
    > the coarse-grained trajectory file. After choosing which index group I want
    > to use, I receive an error message:
    >

- Ignored:
    > I am not familiar with the MARTINI tutorial, but I guess that the
    particles numbers in your traj_cg are different from the one of
    traj_allatoms.
    Thus my suggestion is to check that the numbers reported in the index file
    corresponds to the particles number that you have in your traj_cg.
    The easy way to do it is to look  at  CG_gro file ( you can generate using
    gmx traj in the same way that you have used for traj_cg

    Best regards
    Alessandra



    > Inconsistency in user input: Invalid index group references encountered
    > Group 'bonds_core1' cannot be used in selections, because it contains
    > negative atom indices and/or references atoms not present (largest allowed
    > atom index is 0).
    >
    > The index file itself contains all the proper atom indices. The fact that
    > the error says "largest allowed atom index is 0" makes me think there is an
    > error with my .xtc file, but I did not receive any errors when calculating
    > angle distributions using the exact same trajectory file and appropriate
    > angle index files.
    >
    > Are there any recommendations for how to go about fixing this?
    >
    > Thanks!

Travis Meyer, Ph.D.
INSPIRE Postdoctoral Fellow
Gormley Lab, Rutgers University

From marcelodepolo at gmail.com  Fri Jan 17 23:25:10 2020
From: marcelodepolo at gmail.com (=?UTF-8?Q?Marcelo_Dep=C3=B3lo?=)
Date: Fri, 17 Jan 2020 22:25:10 -0000
Subject: [gmx-users] Residue-Specific CMAPS in GROMACS
Message-ID: <CAFAAhpYPBMAgPdnK-rZx+7GeNvarsP5dXaZQmSCKMr0TqMvpGg@mail.gmail.com>

Hi all,

I've been investigating the implementation of CMAP in GROMACS and, as far
as I understood, the current CMAP format does not allow the use of
residue-specific CMAPS, since it is based on atomtypes and not on function
numbers, as GROMACS normally do.

For example, for AMBER, the function number '9' is defined for dihedral
format:
[ dihedrals ]
;  ai    aj    ak    al funct
    2     1     5     6     9

Considering that FFSB19 (
https://pubs.acs.org/doi/abs/10.1021/acs.jctc.9b00591) uses
residue-specific CMAPs, it I create two different CMAPs for ALA and LEU
residues, it would lead to the same header format for both:

[ cmaptypes ]
C N CT C N 1 24 24\

Therefore, would it be possible to implement the use of function numbers
for CMAPs in GROMACS as well? That dummy '1' could be used as a CMAP ID and
called from the topology designed in .rtp file.

I am not expert in GROMACS code so I would appreciate any inputs that you
may find relevant.

Thanks in advance!
--
Marcelo Depolo Poleto
Postdoctoral Researcher
BIOAGRO - Room T07
Department of General Biology - UFV
Contact: + 55 31 3612-2464

From ashmakhan200 at gmail.com  Sat Jan 18 05:04:44 2020
From: ashmakhan200 at gmail.com (Ashma Khan)
Date: Sat, 18 Jan 2020 04:04:44 -0000
Subject: [gmx-users] Regarding high RMSD
Message-ID: <CAG89CR6Jy8tck0VPC0ZUs80kpV0bSMzqiXmtzCie88A1m+Ow1g@mail.gmail.com>

Thank for your suggestion Alessandra
I have applied the pbc conditions on my system in steps as follows:
1. gmx trjconv -f full_md.xtc -s full_md.tpr -pbc whole -o full_md_whole.xtc
2. gmx trjconv -f full_md_whole.xtc -s first_frame.gro -pbc nojump -o
full_md_nojump.xtc
3. gmx trjconv -f full_md_nojump.xtc -s full_md.tpr -pbc mol -ur compact
-center -o full_md_mol.xtc
After applying all these conditions, peptides of dimer diffusing out of the
box, both in opposite direction at the end of the simulation. kindly
suggest me what should I do.

-- 
Ashma Khan
Research Scholar
Department of Chemistry
AMU, Aligarh

From shaoqingfly1981 at gmail.com  Sat Jan 18 06:27:49 2020
From: shaoqingfly1981 at gmail.com (qing shao)
Date: Sat, 18 Jan 2020 05:27:49 -0000
Subject: [gmx-users] Strange self-coefficient data with "-update gpu" option
Message-ID: <CACSOvHPW_xZX1kdH7ds=Hs69w-FgxRmj58muJWfcKYOos7o_PQ@mail.gmail.com>

Hey,
We ran a quick simulation of a box of 884 spce water model using Gromacs
2020 on a workstation with an RTX 2080 card.
The water box was generated using gmx solvate command.
The whole simulation is 10 ns NPT + 10 ns NVT.
The self-diffusion coefficient is   D[        OW] = 23.5350 (+/- 11.1866)
(1e-5 cm^2/s) if the MD simulation uses the "-update gpu" option
The value turns to normal as D[        OW] = 2.5914 (+/- 0.0069) (1e-5
cm^2/s) without the "-update gpu" option.

Just wondering if anyone observed similar things.

Best,

Qing

From yogesh.rma13 at gmail.com  Sat Jan 18 13:03:20 2020
From: yogesh.rma13 at gmail.com (Yogesh Sharma)
Date: Sat, 18 Jan 2020 12:03:20 -0000
Subject: [gmx-users] Protein pore collapse during simulation.
Message-ID: <CACWq+69Dw_--X1P76syDgz4H0+-cjgc-Fm2yvBeNLkc6x2Qctg@mail.gmail.com>

Hi
I have used inflategro to pack protein in lipid bilayer. While simulation
run protein channel is getting collapsed. can i get some suggestions, if it
is because of the wrong orientation of my protein in bilayer or lesser area
per lipid after shrinking iterations? i have used charmm assembly as
control, where protein channel is fine throughout trajectory. for
inflategro packing i have used 128POPC fom calgiary university website.

I reached an area of 0.67 nm2 while area in upper leaflet was 0.71 and in
lowerleaflet it was 0.70nm2.

  *thanks for your feedback and valuable time*

From aa.hind at hotmail.com  Sat Jan 18 20:12:57 2020
From: aa.hind at hotmail.com (hind ahmed)
Date: Sat, 18 Jan 2020 19:12:57 -0000
Subject: [gmx-users] Hamiltonian replica exchange
Message-ID: <DB8PR10MB26498B2850A889F37748E8C6EA300@DB8PR10MB2649.EURPRD10.PROD.OUTLOOK.COM>

Dear,
is there a tutorial to run Hamiltonian replica exchange in gromacs?? and could you please see if the mdp setting is right to run Hamiltonian replica exchange of lipid system using a coarse-grained method?

 integrator               = sd
tinit                    = 0.0
dt                       = 0.030
nsteps                   = 15000000

nstxout                  = 5000
nstvout                  = 5000
nstfout                  = 5000
nstlog                   = 5000
nstenergy                = 5000
nstxout-compressed       = 5000
compressed-x-precision   = 100

cutoff-scheme            = Verlet
nstlist                  = 20

ns_type                  = grid
pbc                      = xyz
verlet-buffer-tolerance  = 0.005

epsilon_r                = 15
coulombtype              = reaction-field
rcoulomb                 = 1.1
vdw_type                 = cutoff
vdw-modifier             = Potential-shift-verlet
rvdw                     = 1.1

tc-grps                  = membrane solute
tau_t                    = 1.0  1.0
ref_t                    = 323 323

; Pressure coupling:
Pcoupl                   = Parrinello-rahman
Pcoupltype               = isotropic
tau_p                    = 12.0
compressibility          = 4.5e-5
ref_p                    = 1.0

; Free energy control stuff
free_energy              = no
init_lambda_state        = 0
delta_lambda             = 0
calc_lambda_neighbors    = 1        ; only immediate neighboring windows
; Vectors of lambda specified here
; Each combination is an index that is retrieved from init_lambda_state for each simulation
; init_lambda_state        0    1    2    3    4    5    6    7    8    9    10   11
coul-lambdas             = 1.00 0.95 0.90 0.85 0.80 0.75 0.70 0.65 0.60 0.55 0.50 0.45
vdw-lambdas              = 1.00 0.95 0.90 0.85 0.80 0.75 0.70 0.65 0.60 0.55 0.50 0.45
bonded-lambdas           = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
restraint-lambdas        = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00

; Not doing simulated temperting here
temperature_lambdas      = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
; Options for the decoupling
sc-alpha                 = 0.5
sc-coul                  = yes       ; linear interpolation of Coulomb (none in this case)
sc-power                 = 1
sc-sigma                 = 0.3
couple-moltype           = CHOL ; name of moleculetype to decouple
couple-lambda0           = vdw-q      ; only van der Waals interactions
couple-lambda1           = none     ; turn off everything, in this case only vdW
couple-intramol          = no
nstdhdl                  = 10
; Do not generate velocities
gen_vel                  = no
; options for bonds
constraints              = none
; Type of constraint algorithm
constraint-algorithm     = lincs
; Constrain the starting configuration
; since we are continuing from NPT
continuation             = yes
; Highest order in the expansion of the constraint coupling matrix
refcoord_scaling         = all

Regards,
Thanks


From scorpio.liao at gmail.com  Sat Jan 18 21:10:03 2020
From: scorpio.liao at gmail.com (Qinghua Liao)
Date: Sat, 18 Jan 2020 20:10:03 -0000
Subject: [gmx-users] Hamiltonian replica exchange
In-Reply-To: <DB8PR10MB26498B2850A889F37748E8C6EA300@DB8PR10MB2649.EURPRD10.PROD.OUTLOOK.COM>
References: <DB8PR10MB26498B2850A889F37748E8C6EA300@DB8PR10MB2649.EURPRD10.PROD.OUTLOOK.COM>
Message-ID: <dc632f72-f027-e7e2-1327-ff24b2ca89f6@gmail.com>

Hello Hind,

There HREMD is available for Gromacs patched with PLUMED, and there is a 
tutorial you can go through:
https://www.plumed.org/doc-v2.5/user-doc/html/hrex.html


All the best,
Qinghua

On 1/18/20 8:12 PM, hind ahmed wrote:
> Dear,
> is there a tutorial to run Hamiltonian replica exchange in gromacs?? and could you please see if the mdp setting is right to run Hamiltonian replica exchange of lipid system using a coarse-grained method?
>
>   integrator               = sd
> tinit                    = 0.0
> dt                       = 0.030
> nsteps                   = 15000000
>
> nstxout                  = 5000
> nstvout                  = 5000
> nstfout                  = 5000
> nstlog                   = 5000
> nstenergy                = 5000
> nstxout-compressed       = 5000
> compressed-x-precision   = 100
>
> cutoff-scheme            = Verlet
> nstlist                  = 20
>
> ns_type                  = grid
> pbc                      = xyz
> verlet-buffer-tolerance  = 0.005
>
> epsilon_r                = 15
> coulombtype              = reaction-field
> rcoulomb                 = 1.1
> vdw_type                 = cutoff
> vdw-modifier             = Potential-shift-verlet
> rvdw                     = 1.1
>
> tc-grps                  = membrane solute
> tau_t                    = 1.0  1.0
> ref_t                    = 323 323
>
> ; Pressure coupling:
> Pcoupl                   = Parrinello-rahman
> Pcoupltype               = isotropic
> tau_p                    = 12.0
> compressibility          = 4.5e-5
> ref_p                    = 1.0
>
> ; Free energy control stuff
> free_energy              = no
> init_lambda_state        = 0
> delta_lambda             = 0
> calc_lambda_neighbors    = 1        ; only immediate neighboring windows
> ; Vectors of lambda specified here
> ; Each combination is an index that is retrieved from init_lambda_state for each simulation
> ; init_lambda_state        0    1    2    3    4    5    6    7    8    9    10   11
> coul-lambdas             = 1.00 0.95 0.90 0.85 0.80 0.75 0.70 0.65 0.60 0.55 0.50 0.45
> vdw-lambdas              = 1.00 0.95 0.90 0.85 0.80 0.75 0.70 0.65 0.60 0.55 0.50 0.45
> bonded-lambdas           = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> restraint-lambdas        = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
>
> ; Not doing simulated temperting here
> temperature_lambdas      = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> ; Options for the decoupling
> sc-alpha                 = 0.5
> sc-coul                  = yes       ; linear interpolation of Coulomb (none in this case)
> sc-power                 = 1
> sc-sigma                 = 0.3
> couple-moltype           = CHOL ; name of moleculetype to decouple
> couple-lambda0           = vdw-q      ; only van der Waals interactions
> couple-lambda1           = none     ; turn off everything, in this case only vdW
> couple-intramol          = no
> nstdhdl                  = 10
> ; Do not generate velocities
> gen_vel                  = no
> ; options for bonds
> constraints              = none
> ; Type of constraint algorithm
> constraint-algorithm     = lincs
> ; Constrain the starting configuration
> ; since we are continuing from NPT
> continuation             = yes
> ; Highest order in the expansion of the constraint coupling matrix
> refcoord_scaling         = all
>
> Regards,
> Thanks
>


From shlomit.afgin at weizmann.ac.il  Sun Jan 19 10:14:30 2020
From: shlomit.afgin at weizmann.ac.il (Shlomit Afgin)
Date: Sun, 19 Jan 2020 09:14:30 -0000
Subject: [gmx-users] Error: Cannot find AVX 512F compiler flag
In-Reply-To: <CAMNuMATtqS79VKWEtm_rCoix2e4SxWvCOT=16ZXT-_f-3O=duA@mail.gmail.com>
References: <CBF906C1-9C73-46E7-8D4A-9FC14F8030CF@weizmann.ac.il>
	<CANnYEw55zb9uD8j4T7fhhJLh0rNXECZscD30whSpKZNY6H+S4g@mail.gmail.com>
	<8806AC21-F166-46FF-9926-6F44C5CDA7BD@weizmann.ac.il>
	<CAMNuMATtqS79VKWEtm_rCoix2e4SxWvCOT=16ZXT-_f-3O=duA@mail.gmail.com>
Message-ID: <7BCA9356-7EA4-40D7-80F4-43DA3793B1CE@weizmann.ac.il>

It's work okay after I add to the $PATH:

/opt/rh/devtoolset-6/root/usr/bin/gcc



Thanks

Shlomit



?On 16/01/2020, 11:23, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Mark Abraham" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of mark.j.abraham at gmail.com> wrote:



    That tells you what your CPU is capable of. We need to know whether cmake

    has found the compiler that can issue the instructions. Follow the

    suggestions Roland and I have made.



    Mark



    On Wed, 15 Jan 2020 at 10:45, Shlomit Afgin <shlomit.afgin at weizmann.ac.il>

    wrote:



    >

    >

    > I ran:

    >

    > cat /proc/cpuinfo | grep -i avx512

    >

    >

    >

    > and got:

    >

    > avx512f avx512dq avx512cd avx512bw avx512vl

    >

    >

    >

    > So I thought I can use it. Am I wrong?

    >

    >

    >

    > Shlomit

    >

    >

    >

    > On 15/01/2020, 11:14, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se

    > on behalf of Szil?rd P?ll" <

    > gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of

    > pall.szilard at gmail.com> wrote:

    >

    >

    >

    >     Hi,

    >

    >

    >

    >     What hardware are you targeting? Unless you need AVX512 support, you

    > could

    >

    >     just manually specify the appropriate setting in GMX_SIMD, e.g.

    >

    >     -DGMX_SIMD=AVX2_256 would be appropriate for most cases where AVX512

    > is not

    >

    >     supported.

    >

    >

    >

    >     Cheers,

    >

    >     --

    >

    >     Szil?rd

    >

    >

    >

    >

    >

    >     On Wed, Jan 15, 2020 at 9:51 AM Shlomit Afgin <

    > shlomit.afgin at weizmann.ac.il>

    >

    >     wrote:

    >

    >

    >

    >     >

    >

    >     > Hi,

    >

    >     > I tried to install GROMACS 2019.5 on CentOS7,

    >

    >     > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON

    >

    >     >

    >

    >     > I have already installed devtoolset-6 and still get this error:

    >

    >     >

    >

    >     > -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS

    >

    >     > -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Failed

    >

    >     > -- Could not find any flag to build test source (this could be due to

    >

    >     > either the compiler or binutils)

    >

    >     > -- Could not identify number of AVX-512 units - detection program

    > missing

    >

    >     > compilation prerequisites

    >

    >     > -- Could not run code to detect number of AVX-512 FMA units -

    > assuming 2.

    >

    >     > -- Detected best SIMD instructions for this CPU - AVX_512

    >

    >     > CMake Error at cmake/gmxManageSimd.cmake:51 (message):

    >

    >     >   Cannot find AVX 512F compiler flag.  Use a newer compiler, or

    > choose a

    >

    >     >   lower level of SIMD (slower).

    >

    >     > Call Stack (most recent call first):

    >

    >     >   cmake/gmxManageSimd.cmake:186

    >

    >     > (gmx_give_fatal_error_when_simd_support_not_found)

    >

    >     >   CMakeLists.txt:719 (gmx_manage_simd)

    >

    >     >

    >

    >     >

    >

    >     > Thanks,

    >

    >     > Shlomit

    >

    >     > --

    >

    >     > Gromacs Users mailing list

    >

    >     >

    >

    >     > * Please search the archive at

    >

    >     > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

    >

    >     > posting!

    >

    >     >

    >

    >     > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

    >

    >     >

    >

    >     > * For (un)subscribe requests visit

    >

    >     > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users

    > or

    >

    >     > send a mail to gmx-users-request at gromacs.org.

    >

    >     >

    >

    >     --

    >

    >     Gromacs Users mailing list

    >

    >

    >

    >     * Please search the archive at

    > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

    > posting!

    >

    >

    >

    >     * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

    >

    >

    >

    >     * For (un)subscribe requests visit

    >

    >     https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or

    > send a mail to gmx-users-request at gromacs.org.

    > --

    > Gromacs Users mailing list

    >

    > * Please search the archive at

    > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

    > posting!

    >

    > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

    >

    > * For (un)subscribe requests visit

    > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or

    > send a mail to gmx-users-request at gromacs.org.

    --

    Gromacs Users mailing list



    * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!



    * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists



    * For (un)subscribe requests visit

    https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

From roshanpra at gmail.com  Sun Jan 19 11:24:23 2020
From: roshanpra at gmail.com (Roshan Shrestha)
Date: Sun, 19 Jan 2020 10:24:23 -0000
Subject: [gmx-users] Selection/modifying tpr file
Message-ID: <CAGE0GtSiu7N9XdhKE3LXkdkY_RmaifQ0pG4t8C+Na6LSRosUfQ@mail.gmail.com>

Dear all,
              I have a large system, but I want to extract only certain
information from the tpr like make certain selection using index file. Is
there any way I can extract certain information from the tpr file and save
it as another tpr file? Thanks

With best regards

From dallas.warren at monash.edu  Mon Jan 20 04:43:36 2020
From: dallas.warren at monash.edu (Dallas Warren)
Date: Mon, 20 Jan 2020 03:43:36 -0000
Subject: [gmx-users] gmx trjconv
In-Reply-To: <b1688dc90d986f1ee153829c322dadfc@ill.fr>
References: <b1688dc90d986f1ee153829c322dadfc@ill.fr>
Message-ID: <CAOv1qzY1hN8W9f2YbXWeOUZe7dj5S6puVZQLDs+g8ht6bf1-cQ@mail.gmail.com>

This might be a better group of commands:

3 / gmx trjconv -f a.xtc -o a_cluster_center.xtc  -pbc cluster -center
..... select the micelle constructing molecules to cluster and center on,
then System or Non-Water as the output
4 / gmx trjconv -f a_cluster_center.xtc - a_whole.xtc -pbc mol

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Fri, 17 Jan 2020 at 04:53, Giuseppe R Del Sorbo <del-sorbo at ill.fr> wrote:

> Dear users,
>
> I might need an help with gmx trjconv.
>
>
> I have a system with a lysine + a micelle attached on it and I have to
> analyse the radial spherical distribution on the micelle.
>
> The idea is to center the micelle and to work on it.
>
> I used the command "gmx trjconv - cluster" to get a centered micelle and
> if I visualize it in vmd everything is fine.
>
> Accordind with the manual I have to follow this three steps:
>
>
>      1) trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster
>      2) grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr
>      3) trjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump
>
> For the first two steps everything is ok, but for the last one it
> doesnt't work. Gromacs doesn't give any error, but it doesn't run.
>
> Than I tried to write the third step without "-pbc nojump" and it works,
> but the trajectory is a mess and I can also see the lysine, when I
> should only see the micelle..
>
> Do you have any suggestion?
>
> Thanks a lot
>
>
> Giuseppe
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From dallas.warren at monash.edu  Mon Jan 20 04:57:12 2020
From: dallas.warren at monash.edu (Dallas Warren)
Date: Mon, 20 Jan 2020 03:57:12 -0000
Subject: [gmx-users] Selection/modifying tpr file
In-Reply-To: <CAGE0GtSiu7N9XdhKE3LXkdkY_RmaifQ0pG4t8C+Na6LSRosUfQ@mail.gmail.com>
References: <CAGE0GtSiu7N9XdhKE3LXkdkY_RmaifQ0pG4t8C+Na6LSRosUfQ@mail.gmail.com>
Message-ID: <CAOv1qzZ3X31kFC3arCqy=EoYmTCbY7JriZ3QK7mxyohw4apJnw@mail.gmail.com>

You need to rebuild the tpr file using gmx grompp instead, adjusting the
input into it as required (i.e. changing molecules in the input coordinate
file to a subset) to get the output tpr needed.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Sun, 19 Jan 2020 at 21:24, Roshan Shrestha <roshanpra at gmail.com> wrote:

> Dear all,
>               I have a large system, but I want to extract only certain
> information from the tpr like make certain selection using index file. Is
> there any way I can extract certain information from the tpr file and save
> it as another tpr file? Thanks
>
> With best regards
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From pragati2325 at gmail.com  Mon Jan 20 06:50:51 2020
From: pragati2325 at gmail.com (Pragati Sharma)
Date: Mon, 20 Jan 2020 05:50:51 -0000
Subject: [gmx-users] Uniaxial elongation using deform option
Message-ID: <CAMpF9Q0aXLzCxff6fgJt=CTbwnMsWjq_rTf21ohAfx7LO8P1MQ@mail.gmail.com>

Dear all,

I want to calculate young's modulus of a polymer using uniaxial elongation.
(elongation in z axis but no volume change)
I am using 'deform' option and semiisotropic pressure coupling and zero
compressibility in z for that.
My mdp parameters ar:










*Pcoupl                   = BerendsenPcoupltype            =
semiisotropictau_p                     = 1compressibility       = 4.5e-5
0ref_p                       = 1 1gen_vel                    = nogen_temp
              = 298; options for non-eq viscosity calcdeform = 0 0 0.001 0
0 0refcoord_scaling = com*

Since elongation is in z axis, Lz increases, and Lx and Ly decreases, but
the decrease in these two axis is less compared to increase in Lz, and so
my volume is not conserved, it is increasing.

Can anyone suggest me some way for uniaxial elongation in gromacs, but
volume should not change

Thanks!

From ericirrgang at gmail.com  Mon Jan 20 11:28:02 2020
From: ericirrgang at gmail.com (Eric Irrgang)
Date: Mon, 20 Jan 2020 10:28:02 -0000
Subject: [gmx-users] Ran into trouble installing Gromacs API
In-Reply-To: <mailman.793.1579267153.1966.gromacs.org_gmx-users@maillist.sys.kth.se>
References: <mailman.793.1579267153.1966.gromacs.org_gmx-users@maillist.sys.kth.se>
Message-ID: <CANMuMvk2faBZdhQMLR8aY4Pa0GZ0G1Wsx8rNZWXKVy3N09w35Q@mail.gmail.com>

Hi Marko,

I'm sorry for the confusion. The install instructions for gmxapi 0.1 on
GROMACS 2020 are at
http://manual.gromacs.org/current/gmxapi/userguide/install.html

I plan to update readthedocs in the next few days to cover both gmxapi
0.0.7 on GROMACS 2019 and gmxapi 0.1 (
https://github.com/kassonlab/gmxapi/issues/249), but I see that the
reorganization of the repository leads to extra confusion (as you describe)
so I will also update the old install docs. (
https://github.com/kassonlab/gmxapi/issues/252)

To help me understand documentation navigation issues better, can you tell
me how you ended up at the readthedocs.io site while installing GROMACS
2020?

From: Marko Petrovic <marko at kth.se>
> Subject: [gmx-users] Ran into trouble installing Gromacs API
>
> Hello
>
> I have (I think successfully) installed Gromacs 2020 on my computer (MacOS
> X Catalina) and tried to install the API using the quick install guide:
> https://gmxapi.readthedocs.io/en/latest/quickstart.html
> and get stuck on the step:
>
> pip install -r requirements.txt
>
> as that file does not seem to be in that folder of the repo. I found the
> file "requirements-test.txt" in the folder "python-packaging" and tried
> with that but got a long error message of missing stuff I didn't
> understand, I'm hoping those error messages are from the file not being
> intended for use inn the manner I tried so I'm currently not including
> those here.
>
> Should I have installed gromacs 2019 for which the API was developed? Has
> anyone else installed the API recently and (hopefully) exxperienced and
> overcome this hurdle?
>
> With Regards
> Marko Petrovic
> Educator
> Computational Science and Technology
> School of Electrical Engineering and Computer Science
> KTH Royal Institute of Technology
>
>

From sinaomrani96 at gmail.com  Mon Jan 20 12:02:14 2020
From: sinaomrani96 at gmail.com (Sina Omrani)
Date: Mon, 20 Jan 2020 11:02:14 -0000
Subject: [gmx-users] State of Matter
Message-ID: <CADp8ML7de6nHPY=gDxU+6Ku4j75ue3RYVM9U1zgqet8ekCxHrg@mail.gmail.com>

Hi, I'm new to GROMACS and Molecular Dynamics and I'm sorry if it is a
witless question but how we can specify the state of a component (gas,
liquid or super critical) in MD simulations?

From blau at kth.se  Mon Jan 20 13:12:20 2020
From: blau at kth.se (Christian Blau)
Date: Mon, 20 Jan 2020 12:12:20 -0000
Subject: [gmx-users] State of Matter
In-Reply-To: <CADp8ML7de6nHPY=gDxU+6Ku4j75ue3RYVM9U1zgqet8ekCxHrg@mail.gmail.com>
References: <CADp8ML7de6nHPY=gDxU+6Ku4j75ue3RYVM9U1zgqet8ekCxHrg@mail.gmail.com>
Message-ID: <c04e6e91-84e5-917d-87ab-4cac11911478@kth.se>

Hi Sina,


You can have a look at order parameters of your system like angular distributions, orientations, local densities, etc. 
with analysis tools like gmx angle, h2order, order.


Best,

Christian

On 2020-01-20 12:02, Sina Omrani wrote:
> Hi, I'm new to GROMACS and Molecular Dynamics and I'm sorry if it is a
> witless question but how we can specify the state of a component (gas,
> liquid or super critical) in MD simulations?

From sunyeping at aliyun.com  Mon Jan 20 14:03:40 2020
From: sunyeping at aliyun.com (sunyeping)
Date: Mon, 20 Jan 2020 13:03:40 -0000
Subject: [gmx-users] =?utf-8?q?how_to_include_multiple_energy_groups_for_i?=
 =?utf-8?q?nteraction_energy_calculation=3F?=
Message-ID: <d2374645-1e09-4c7d-aabe-9028643f00f6.sunyeping@aliyun.com>

Dear all,

I am doing MD simulations on a protein-ligand complex. This complex has 4  protein subunits, with each subunits binding one ligand, so there are 4 ligands (named LIG1, LIG2, LIG3 and LIG4, respectively) in it. I have finished the production run and get a trajectory, and now I want to calculate the interaction energy between each ligand and their binding protein subunit, respectively. I include the  "energygrps" parameter in the mdp file for generating a tpr file for rerun the trajectory as following:
    energygrps      =  Protein LIG1

This seems to work fine. However, could it be possible to include all four ligands in the "energygrps" parameter and rerun the trajectory once to get the interaction energy between all the four ligands and their respective binding protein subunit? I tried to write the "energygrps" parameter as following:
  energygrps      =  Protein LIG1, Protein LIG2, Protein LIG3, Protein LIG4
and run the "grompp" command:
     gmx grompp -f ie.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o ie.tpr
I received the following error:
    Fatal error:
Group LIG1, referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp.

I am sure that LIG1 is included in the index file. This error is most probably caused by the incorrect input of the "energygrps" parameter in the mdp file. 

So I wonder whether it is possible to include multiple energy groups in the mdp file or I have to rerun the trajectory four times to get the interaction energy for the four ligands?

Thank you in advance.

Yeping Sun

From blau at kth.se  Mon Jan 20 14:18:25 2020
From: blau at kth.se (Christian Blau)
Date: Mon, 20 Jan 2020 13:18:25 -0000
Subject: [gmx-users] specific heat calculation using "gmx dos"
In-Reply-To: <CAMpF9Q1NQK_aMZK44qA6RDaOigvxHhfSkCnkyBcQ5GeLtHtRAA@mail.gmail.com>
References: <CAMpF9Q1NQK_aMZK44qA6RDaOigvxHhfSkCnkyBcQ5GeLtHtRAA@mail.gmail.com>
Message-ID: <867f4c8e-de05-6027-4282-eb02909c89a5@kth.se>

Hi Pragati,


Answers in short:

1. It's only c_v, you'll have to add VT \alpha_T^2/ \kappa_T to obtain c_p

2. I suggest you use the approach in the paper, running an NVT simulation and base all on the c_v estimate.

3. To check convergence, I suggest running the analysis again on shorter parts of your trajectory (1/2 of the data, 1/4 
of the data etc.)

4. You'll not see the quantum correction with this approach, your force-field might rely on entropy- enthalpy 
compensation. I would guess that you would obtain worse results with such an approach.


The DOS tool follows the supplementary material S(1)-S(17) in "Force Field Benchmark of Organic Liquids: Density, 
Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion 
Coefficient, and Dielectric Constant" by

Carl Caleman, Paul J. van Maaren, Minyan Hong, Jochen S. Hub, Luciano T. Costa, David van der Spoel. It's output "Heat 
capacity ... J/mol K" corresponds to equation (14) in above publication, the constant volume heat capacity c_v *with* 
quantum correction. To obtain c_p you would still need to apply (eqn 12).


Best,

Christian


On 2020-01-03 07:33, Pragati Sharma wrote:
>   Dear all,
>
> I am trying to calculate heat capacity of a polymeric system (30k atoms)
> using gromacs.
> I tried the classical way from the fluctuation dependent properties using
> "gmx energy", but the values are not matching experimental values.
>
> I want to use "gmx dos" program, but I have some confusions.
>
> 1. Does it gives only the quantum corrections in heat capacity, which
> should be added to the one calculated from 'gmx energy' or  Does it gives
> full heat capacity value including quantum corrections.
>
> 2. Should I have to run NVT simulations, run gmx dos, find Cv and the add
> then calculate Cp, as given in the paper ( J. Chem. Theory Comput. 2012, 8,
> 61?74), *OR*
> I can run a NPT simulation and calculate Cp from gmx dos.
>
> 3. gmx dos gives the Cp/Cv value in "dos.log" file. but is there any output
> file to check its convergence. I mean how should I decide, how long the
> trajectory I should take.
>
> 4. Cp can be calculated from the slope of enthalpy vs temp plot (dH/dT) (in
> a small range of temp), what limitation does this approach have.
>
> Thanks in advance.

From sinaomrani96 at gmail.com  Mon Jan 20 15:14:15 2020
From: sinaomrani96 at gmail.com (Sina Omrani)
Date: Mon, 20 Jan 2020 14:14:15 -0000
Subject: [gmx-users] State of Matter
In-Reply-To: <c04e6e91-84e5-917d-87ab-4cac11911478@kth.se>
References: <CADp8ML7de6nHPY=gDxU+6Ku4j75ue3RYVM9U1zgqet8ekCxHrg@mail.gmail.com>
	<c04e6e91-84e5-917d-87ab-4cac11911478@kth.se>
Message-ID: <CADp8ML5pr7SDxV4Excu-y3mi+MZvV_f-3hGAVwMPPP2mW8v48g@mail.gmail.com>

Thank you Christian,
But my question is more about how to introduce state of the system. Does it
depend on the temperature and pressure or force field parameters?

On Mon, 20 Jan 2020 at 15:42, Christian Blau <blau at kth.se> wrote:

> Hi Sina,
>
>
> You can have a look at order parameters of your system like angular
> distributions, orientations, local densities, etc.
> with analysis tools like gmx angle, h2order, order.
>
>
> Best,
>
> Christian
>
> On 2020-01-20 12:02, Sina Omrani wrote:
> > Hi, I'm new to GROMACS and Molecular Dynamics and I'm sorry if it is a
> > witless question but how we can specify the state of a component (gas,
> > liquid or super critical) in MD simulations?
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From jalemkul at vt.edu  Mon Jan 20 15:16:00 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Mon, 20 Jan 2020 14:16:00 -0000
Subject: [gmx-users] State of Matter
In-Reply-To: <CADp8ML5pr7SDxV4Excu-y3mi+MZvV_f-3hGAVwMPPP2mW8v48g@mail.gmail.com>
References: <CADp8ML7de6nHPY=gDxU+6Ku4j75ue3RYVM9U1zgqet8ekCxHrg@mail.gmail.com>
	<c04e6e91-84e5-917d-87ab-4cac11911478@kth.se>
	<CADp8ML5pr7SDxV4Excu-y3mi+MZvV_f-3hGAVwMPPP2mW8v48g@mail.gmail.com>
Message-ID: <4bd604bc-b0bc-22b1-4639-3b8bd2b3cfcf@vt.edu>



On 1/20/20 9:14 AM, Sina Omrani wrote:
> Thank you Christian,
> But my question is more about how to introduce state of the system. Does it
> depend on the temperature and pressure or force field parameters?

Yes, all of them. There is no input parameter that says "this material 
is a solid/liquid/gas." The outcome of the simulation is entirely 
dependent upon the thermodynamic parameters and the quality of the force 
field in simulating the given species under those conditions.

-Justin

> On Mon, 20 Jan 2020 at 15:42, Christian Blau <blau at kth.se> wrote:
>
>> Hi Sina,
>>
>>
>> You can have a look at order parameters of your system like angular
>> distributions, orientations, local densities, etc.
>> with analysis tools like gmx angle, h2order, order.
>>
>>
>> Best,
>>
>> Christian
>>
>> On 2020-01-20 12:02, Sina Omrani wrote:
>>> Hi, I'm new to GROMACS and Molecular Dynamics and I'm sorry if it is a
>>> witless question but how we can specify the state of a component (gas,
>>> liquid or super critical) in MD simulations?
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From jalemkul at vt.edu  Mon Jan 20 15:17:07 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Mon, 20 Jan 2020 14:17:07 -0000
Subject: [gmx-users] how to include multiple energy groups for
 interaction energy calculation?
In-Reply-To: <d2374645-1e09-4c7d-aabe-9028643f00f6.sunyeping@aliyun.com>
References: <d2374645-1e09-4c7d-aabe-9028643f00f6.sunyeping@aliyun.com>
Message-ID: <e932d046-f430-acf0-e98c-ef106544384b@vt.edu>



On 1/20/20 7:58 AM, sunyeping wrote:
> Dear all,
>
> I am doing MD simulations on a protein-ligand complex. This complex has 4  protein subunits, with each subunits binding one ligand, so there are 4 ligands (named LIG1, LIG2, LIG3 and LIG4, respectively) in it. I have finished the production run and get a trajectory, and now I want to calculate the interaction energy between each ligand and their binding protein subunit, respectively. I include the  "energygrps" parameter in the mdp file for generating a tpr file for rerun the trajectory as following:
>      energygrps      =  Protein LIG1
>
> This seems to work fine. However, could it be possible to include all four ligands in the "energygrps" parameter and rerun the trajectory once to get the interaction energy between all the four ligands and their respective binding protein subunit? I tried to write the "energygrps" parameter as following:
>    energygrps      =  Protein LIG1, Protein LIG2, Protein LIG3, Protein LIG4
> and run the "grompp" command:
>       gmx grompp -f ie.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o ie.tpr
> I received the following error:
>      Fatal error:
> Group LIG1, referenced in the .mdp file was not found in the index file.
> Group names must match either [moleculetype] names or custom index group
> names, in which case you must supply an index file to the '-n' option
> of grompp.
>
> I am sure that LIG1 is included in the index file. This error is most probably caused by the incorrect input of the "energygrps" parameter in the mdp file.
>
> So I wonder whether it is possible to include multiple energy groups in the mdp file or I have to rerun the trajectory four times to get the interaction energy for the four ligands?

The list of energygrps should not be comma-delimited. You should specify:

energygrps = Protein LIG1 LIG2 LIG3 LIG4

and this will generate a full matrix of interactions among all four 
species. The LIG1-LIG2, LIG1-LIG3, etc. may not be interesting to you 
but this is how you get all of the interaction energies with the protein 
in one shot.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From jalemkul at vt.edu  Mon Jan 20 15:17:44 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Mon, 20 Jan 2020 14:17:44 -0000
Subject: [gmx-users] Selection/modifying tpr file
In-Reply-To: <CAGE0GtSiu7N9XdhKE3LXkdkY_RmaifQ0pG4t8C+Na6LSRosUfQ@mail.gmail.com>
References: <CAGE0GtSiu7N9XdhKE3LXkdkY_RmaifQ0pG4t8C+Na6LSRosUfQ@mail.gmail.com>
Message-ID: <b549ff3a-ecb8-f9c3-383d-ad0a5a9a59bb@vt.edu>



On 1/19/20 5:24 AM, Roshan Shrestha wrote:
> Dear all,
>                I have a large system, but I want to extract only certain
> information from the tpr like make certain selection using index file. Is
> there any way I can extract certain information from the tpr file and save
> it as another tpr file? Thanks

You can select a subset of the system via convert-tpr with a suitable 
index file. All other information (topology, force field, run settings) 
will stay the same.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From jalemkul at vt.edu  Mon Jan 20 15:18:48 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Mon, 20 Jan 2020 14:18:48 -0000
Subject: [gmx-users] Protein pore collapse during simulation.
In-Reply-To: <CACWq+69Dw_--X1P76syDgz4H0+-cjgc-Fm2yvBeNLkc6x2Qctg@mail.gmail.com>
References: <CACWq+69Dw_--X1P76syDgz4H0+-cjgc-Fm2yvBeNLkc6x2Qctg@mail.gmail.com>
Message-ID: <ae296a98-5dec-28a9-f7f8-c0f49d805b78@vt.edu>



On 1/18/20 7:03 AM, Yogesh Sharma wrote:
> Hi
> I have used inflategro to pack protein in lipid bilayer. While simulation
> run protein channel is getting collapsed. can i get some suggestions, if it
> is because of the wrong orientation of my protein in bilayer or lesser area
> per lipid after shrinking iterations? i have used charmm assembly as
> control, where protein channel is fine throughout trajectory. for
> inflategro packing i have used 128POPC fom calgiary university website.
>
> I reached an area of 0.67 nm2 while area in upper leaflet was 0.71 and in
> lowerleaflet it was 0.70nm2.
>
>    *thanks for your feedback and valuable time*

You've got many variables here. Are the number of lipids the same? The 
number of waters? Was each system equilibrated sufficiently to yield a 
stable state before the simulation started? The CHARMM-GUI methodology 
is far more robust than using InflateGRO and the C36 force field is much 
more accurate than the ancient Berger parameters.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From jalemkul at vt.edu  Mon Jan 20 15:20:16 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Mon, 20 Jan 2020 14:20:16 -0000
Subject: [gmx-users] Regarding high RMSD
In-Reply-To: <CAG89CR6Jy8tck0VPC0ZUs80kpV0bSMzqiXmtzCie88A1m+Ow1g@mail.gmail.com>
References: <CAG89CR6Jy8tck0VPC0ZUs80kpV0bSMzqiXmtzCie88A1m+Ow1g@mail.gmail.com>
Message-ID: <b1d1dbc4-370a-3548-7184-914da9dce68a@vt.edu>



On 1/17/20 11:01 PM, Ashma Khan wrote:
> Thank for your suggestion Alessandra
> I have applied the pbc conditions on my system in steps as follows:
> 1. gmx trjconv -f full_md.xtc -s full_md.tpr -pbc whole -o full_md_whole.xtc
> 2. gmx trjconv -f full_md_whole.xtc -s first_frame.gro -pbc nojump -o
> full_md_nojump.xtc
> 3. gmx trjconv -f full_md_nojump.xtc -s full_md.tpr -pbc mol -ur compact
> -center -o full_md_mol.xtc
> After applying all these conditions, peptides of dimer diffusing out of the
> box, both in opposite direction at the end of the simulation. kindly
> suggest me what should I do.
>

Center on one peptide only, to see if the other is re-wrapped in the 
central image along with it. If not, then you do not have a dimer at all 
times and the RMSD should be high. If they stay associated, re-calculate 
RMSD because the previous results were just a PBC artifact in that case. 
With any multimeric system, you cannot just center on "Protein" because 
the geometric center of the group can be exactly coincident with the 
center of the box with all the proteins at different faces/corners of 
the unit cell.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From imaneternity at gmail.com  Mon Jan 20 15:28:14 2020
From: imaneternity at gmail.com (Iman Katouzian)
Date: Mon, 20 Jan 2020 14:28:14 -0000
Subject: [gmx-users] dssp version of gromacs 2019.3
Message-ID: <CALipc=pGFR7QtP+7Kt+6PCHbe9bpUj2BEG5N4bhZs9TjU8fBHw@mail.gmail.com>

Good day,
I have downloaded the latest version of DSSP from the site :
https://swift.cmbi.umcn.nl/gv/dssp/
<https://www.researchgate.net/deref/https%3A%2F%2Fswift.cmbi.umcn.nl%2Fgv%2Fdssp%2F>
however
as I downloaded and extract the package I see it is named hssp 1.3.4 and
the codes are different from dssp that determines the secondary structures
in gromacs using gmx do_dssp!
can somebody help me on this issue and send me the latest version of DSSP
for gromacs 2019.3 so that I can make it executable and do my task. As I
run it with older version of dssp it reads the code and starts reading the
frames, however even after 2 hours nothing happens and the frame is still
zero!
Many thanks

-- 

*Iman Katouzian*

*Ph.D.** candidate of Food Process Engineering*

*Faculty of Food Science and Technology*

*University of Agricultural Sciences and Natural Resources, Gorgan, Iran*

From gmxquestions at gmail.com  Mon Jan 20 15:48:39 2020
From: gmxquestions at gmail.com (Gmx QA)
Date: Mon, 20 Jan 2020 14:48:39 -0000
Subject: [gmx-users] RDF between larger molecules
Message-ID: <CANftEdOzsa1UbhLh3NghZbps76kZuEm=1LrT=TLTt_9JF796-g@mail.gmail.com>

Hi list,

I am working on a system that contains lipids, but since there is no water
present they do not form a typical bilayer.

In these systems I also have some smaller drug-like molecules. What would
be the best way to get a proper rdf-function between the lipids and the
drugs? Since both types of molecules are larger than single atoms, I tried
to calculate a com-com rdf using

-selrpos whole_mol_com -seltype whole_mol_com

but the resulting curve is very rugged (i.e. not as smooth as
the atom-rdf's typically shown). The minimum distance (the distance
below which the pdf is zero) also appears to be quite small, since one the
molecules is a lipid I would have expected a larger distance than
the corresponding value seen in e.g. an oxygen-oxygen rdf for water.

Might all of this be consequences of the fact that I have a com-com rdf
between a limited number of molecules?

Thanks
/PK

From jalemkul at vt.edu  Mon Jan 20 15:50:20 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Mon, 20 Jan 2020 14:50:20 -0000
Subject: [gmx-users] RDF between larger molecules
In-Reply-To: <CANftEdOzsa1UbhLh3NghZbps76kZuEm=1LrT=TLTt_9JF796-g@mail.gmail.com>
References: <CANftEdOzsa1UbhLh3NghZbps76kZuEm=1LrT=TLTt_9JF796-g@mail.gmail.com>
Message-ID: <1aeb1d39-af3c-f31e-40ee-00f7b613f130@vt.edu>



On 1/20/20 9:48 AM, Gmx QA wrote:
> Hi list,
>
> I am working on a system that contains lipids, but since there is no water
> present they do not form a typical bilayer.
>
> In these systems I also have some smaller drug-like molecules. What would
> be the best way to get a proper rdf-function between the lipids and the
> drugs? Since both types of molecules are larger than single atoms, I tried
> to calculate a com-com rdf using
>
> -selrpos whole_mol_com -seltype whole_mol_com
>
> but the resulting curve is very rugged (i.e. not as smooth as
> the atom-rdf's typically shown). The minimum distance (the distance
> below which the pdf is zero) also appears to be quite small, since one the
> molecules is a lipid I would have expected a larger distance than
> the corresponding value seen in e.g. an oxygen-oxygen rdf for water.
>
> Might all of this be consequences of the fact that I have a com-com rdf
> between a limited number of molecules?

Yes, likely. You could in principle have a COM-COM RDF value very close 
to r=0 if a lipid were to wrap around a drug molecule, so I don't think 
any of your results are unexpected.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From gmxquestions at gmail.com  Mon Jan 20 16:01:25 2020
From: gmxquestions at gmail.com (Gmx QA)
Date: Mon, 20 Jan 2020 15:01:25 -0000
Subject: [gmx-users] RDF between larger molecules
In-Reply-To: <1aeb1d39-af3c-f31e-40ee-00f7b613f130@vt.edu>
References: <CANftEdOzsa1UbhLh3NghZbps76kZuEm=1LrT=TLTt_9JF796-g@mail.gmail.com>
	<1aeb1d39-af3c-f31e-40ee-00f7b613f130@vt.edu>
Message-ID: <CANftEdMYJzY6XR44FMBSoMvuz4X8ZNWHsJjHwaDFCchfXHgoLA@mail.gmail.com>

Thanks Justin!

Can you also comment on the other issue, the lack of smoothness? I guess
this is because I don't have that many individual coms per bin to
accurately compute the rdf? At least I think that makes sense since when I
increase the value of -bin in gmx rdf I get an increase in "smoothness" and
fewer "jump" back and forth.



Den m?n 20 jan. 2020 kl 15:50 skrev Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 1/20/20 9:48 AM, Gmx QA wrote:
> > Hi list,
> >
> > I am working on a system that contains lipids, but since there is no
> water
> > present they do not form a typical bilayer.
> >
> > In these systems I also have some smaller drug-like molecules. What would
> > be the best way to get a proper rdf-function between the lipids and the
> > drugs? Since both types of molecules are larger than single atoms, I
> tried
> > to calculate a com-com rdf using
> >
> > -selrpos whole_mol_com -seltype whole_mol_com
> >
> > but the resulting curve is very rugged (i.e. not as smooth as
> > the atom-rdf's typically shown). The minimum distance (the distance
> > below which the pdf is zero) also appears to be quite small, since one
> the
> > molecules is a lipid I would have expected a larger distance than
> > the corresponding value seen in e.g. an oxygen-oxygen rdf for water.
> >
> > Might all of this be consequences of the fact that I have a com-com rdf
> > between a limited number of molecules?
>
> Yes, likely. You could in principle have a COM-COM RDF value very close
> to r=0 if a lipid were to wrap around a drug molecule, so I don't think
> any of your results are unexpected.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From jalemkul at vt.edu  Mon Jan 20 16:02:53 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Mon, 20 Jan 2020 15:02:53 -0000
Subject: [gmx-users] RDF between larger molecules
In-Reply-To: <CANftEdMYJzY6XR44FMBSoMvuz4X8ZNWHsJjHwaDFCchfXHgoLA@mail.gmail.com>
References: <CANftEdOzsa1UbhLh3NghZbps76kZuEm=1LrT=TLTt_9JF796-g@mail.gmail.com>
	<1aeb1d39-af3c-f31e-40ee-00f7b613f130@vt.edu>
	<CANftEdMYJzY6XR44FMBSoMvuz4X8ZNWHsJjHwaDFCchfXHgoLA@mail.gmail.com>
Message-ID: <a5b11e81-22da-2010-d200-e4779876d6cb@vt.edu>



On 1/20/20 10:00 AM, Gmx QA wrote:
> Thanks Justin!
>
> Can you also comment on the other issue, the lack of smoothness? I guess
> this is because I don't have that many individual coms per bin to
> accurately compute the rdf? At least I think that makes sense since when I
> increase the value of -bin in gmx rdf I get an increase in "smoothness" and
> fewer "jump" back and forth.
>

It's just sampling. RDF analysis was designed for pure liquids, in which 
there are a huge number of the same type of interaction. You have a 
heterogeneous system, so in the absence of much longer simulations, 
you're not going to get smooth RDFs.

-Justin

>
> Den m?n 20 jan. 2020 kl 15:50 skrev Justin Lemkul <jalemkul at vt.edu>:
>
>>
>> On 1/20/20 9:48 AM, Gmx QA wrote:
>>> Hi list,
>>>
>>> I am working on a system that contains lipids, but since there is no
>> water
>>> present they do not form a typical bilayer.
>>>
>>> In these systems I also have some smaller drug-like molecules. What would
>>> be the best way to get a proper rdf-function between the lipids and the
>>> drugs? Since both types of molecules are larger than single atoms, I
>> tried
>>> to calculate a com-com rdf using
>>>
>>> -selrpos whole_mol_com -seltype whole_mol_com
>>>
>>> but the resulting curve is very rugged (i.e. not as smooth as
>>> the atom-rdf's typically shown). The minimum distance (the distance
>>> below which the pdf is zero) also appears to be quite small, since one
>> the
>>> molecules is a lipid I would have expected a larger distance than
>>> the corresponding value seen in e.g. an oxygen-oxygen rdf for water.
>>>
>>> Might all of this be consequences of the fact that I have a com-com rdf
>>> between a limited number of molecules?
>> Yes, likely. You could in principle have a COM-COM RDF value very close
>> to r=0 if a lipid were to wrap around a drug molecule, so I don't think
>> any of your results are unexpected.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From aharongomez at udec.cl  Mon Jan 20 18:08:37 2020
From: aharongomez at udec.cl (Aharon Gomez)
Date: Mon, 20 Jan 2020 17:08:37 -0000
Subject: [gmx-users] Making an index file for specific solvent molecules
Message-ID: <14A9B831-779B-4121-9F4F-232484DC4B0C@getmailspring.com>

Hi everyone,

I'm working on gas like molecules diffusion in protein. I have an equilibrated system and now I want
to replace solvent molecules with some other molecule, like O2, but i want to select just the water molecules
that are placed over some distance to my protein.
Is there any built in tool in gromacs to make an index file of these solvent molecules or any other way to do it?

Aharon Gomez Llanos
Estudiante de Doctorado en Ciencias c/m en Qu?mica
Universidad de Concepci?n


From jalemkul at vt.edu  Mon Jan 20 21:23:11 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Mon, 20 Jan 2020 20:23:11 -0000
Subject: [gmx-users] Making an index file for specific solvent molecules
In-Reply-To: <14A9B831-779B-4121-9F4F-232484DC4B0C@getmailspring.com>
References: <14A9B831-779B-4121-9F4F-232484DC4B0C@getmailspring.com>
Message-ID: <33fef495-7d3d-2116-0d62-890aac4117a3@vt.edu>



On 1/20/20 11:31 AM, Aharon Gomez wrote:
> Hi everyone,
>
> I'm working on gas like molecules diffusion in protein. I have an equilibrated system and now I want
> to replace solvent molecules with some other molecule, like O2, but i want to select just the water molecules
> that are placed over some distance to my protein.
> Is there any built in tool in gromacs to make an index file of these solvent molecules or any other way to do it?

You can use gmx select to select atoms/molecules based on distance 
criteria. See syntax examples with "gmx help selections"

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From sunyeping at aliyun.com  Tue Jan 21 08:06:19 2020
From: sunyeping at aliyun.com (sunyeping)
Date: Tue, 21 Jan 2020 07:06:19 -0000
Subject: [gmx-users]
 =?utf-8?q?how_to_include_multiple_energy_groups_for_i?=
 =?utf-8?q?nteraction_energy_calculation=3F?=
In-Reply-To: <e932d046-f430-acf0-e98c-ef106544384b@vt.edu>
References: <d2374645-1e09-4c7d-aabe-9028643f00f6.sunyeping@aliyun.com>,
	<e932d046-f430-acf0-e98c-ef106544384b@vt.edu>
Message-ID: <047545aa-e2af-46f4-9d2b-0796df0a8c6b.sunyeping@aliyun.com>

Hi Justin,

Thank you for reply. "energygrps = Protein LIG1 LIG2 LIG3 LIG4" can do the work. I still have a couple of questions: 

(1) When using the "gmx energy -f ie.edr -o ie.xvg" to extract the interaction energy, the interested energy terms should be input. Because there are four ligands in my structure, there are accordingly 16 terms, for example, 22 Coul-SR:Protein-LIG1, 23 LJ-SR:Protein-LIG1, 24 Coul-14:Protein-LIG1 and 25 LJ-14-LIG1 etc.. I can input the no. of these 16 terms one by one as "22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37", but is there a simple syntax for this selection? I tried "22 to 37" and "22-37", but they doesn't work.

(2) I find that the values of  all  Coul-14 and LJ-14 terms are zero. Does this make any sense?

Best,

Yeping Sun
------------------------------------------------------------------
From:Justin Lemkul <jalemkul at vt.edu>
Sent At:2020 Jan. 20 (Mon.) 22:17
To:gromacs <gmx-users at gromacs.org>; ??? <sunyeping at aliyun.com>
Subject:Re: [gmx-users] how to include multiple energy groups for interaction energy calculation?



On 1/20/20 7:58 AM, sunyeping wrote:
> Dear all,
>
> I am doing MD simulations on a protein-ligand complex. This complex has 4  protein subunits, with each subunits binding one ligand, so there are 4 ligands (named LIG1, LIG2, LIG3 and LIG4, respectively) in it. I have finished the production run and get a trajectory, and now I want to calculate the interaction energy between each ligand and their binding protein subunit, respectively. I include the  "energygrps" parameter in the mdp file for generating a tpr file for rerun the trajectory as following:
>      energygrps      =  Protein LIG1
>
> This seems to work fine. However, could it be possible to include all four ligands in the "energygrps" parameter and rerun the trajectory once to get the interaction energy between all the four ligands and their respective binding protein subunit? I tried to write the "energygrps" parameter as following:
>    energygrps      =  Protein LIG1, Protein LIG2, Protein LIG3, Protein LIG4
> and run the "grompp" command:
>       gmx grompp -f ie.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o ie.tpr
> I received the following error:
>      Fatal error:
> Group LIG1, referenced in the .mdp file was not found in the index file.
> Group names must match either [moleculetype] names or custom index group
> names, in which case you must supply an index file to the '-n' option
> of grompp.
>
> I am sure that LIG1 is included in the index file. This error is most probably caused by the incorrect input of the "energygrps" parameter in the mdp file.
>
> So I wonder whether it is possible to include multiple energy groups in the mdp file or I have to rerun the trajectory four times to get the interaction energy for the four ligands?

The list of energygrps should not be comma-delimited. You should specify:

energygrps = Protein LIG1 LIG2 LIG3 LIG4

and this will generate a full matrix of interactions among all four 
species. The LIG1-LIG2, LIG1-LIG3, etc. may not be interesting to you 
but this is how you get all of the interaction energies with the protein 
in one shot.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================

From alashkov83 at gmail.com  Tue Jan 21 08:19:39 2020
From: alashkov83 at gmail.com (=?UTF-8?B?0JDQu9C10LrRgdCw0L3QtNGAINCb0LDRiNC60L7Qsg==?=)
Date: Tue, 21 Jan 2020 07:19:39 -0000
Subject: [gmx-users] how to include multiple energy groups for
 interaction energy calculation?
In-Reply-To: <047545aa-e2af-46f4-9d2b-0796df0a8c6b.sunyeping@aliyun.com>
References: <d2374645-1e09-4c7d-aabe-9028643f00f6.sunyeping@aliyun.com>
	<e932d046-f430-acf0-e98c-ef106544384b@vt.edu>
	<047545aa-e2af-46f4-9d2b-0796df0a8c6b.sunyeping@aliyun.com>
Message-ID: <CACc8-jxQU+1pVmt7KNsD2GPTvVVJ4AGDuSQpD-YH3hfLZ1JQkQ@mail.gmail.com>

This ok. This term show non-bonded interaction for atoms
located through two valence bonds.
Alex

??, 21 ???. 2020 ?. ? 10:06, sunyeping <sunyeping at aliyun.com>:

> Hi Justin,
>
> Thank you for reply. "energygrps = Protein LIG1 LIG2 LIG3 LIG4" can do the
> work. I still have a couple of questions:
>
> (1) When using the "gmx energy -f ie.edr -o ie.xvg" to extract the
> interaction energy, the interested energy terms should be input. Because
> there are four ligands in my structure, there are accordingly 16 terms, for
> example, 22 Coul-SR:Protein-LIG1, 23 LJ-SR:Protein-LIG1, 24
> Coul-14:Protein-LIG1 and 25 LJ-14-LIG1 etc.. I can input the no. of these
> 16 terms one by one as "22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37",
> but is there a simple syntax for this selection? I tried "22 to 37" and
> "22-37", but they doesn't work.
>
> (2) I find that the values of  all  Coul-14 and LJ-14 terms are zero. Does
> this make any sense?
>
> Best,
>
> Yeping Sun
> ------------------------------------------------------------------
> From:Justin Lemkul <jalemkul at vt.edu>
> Sent At:2020 Jan. 20 (Mon.) 22:17
> To:gromacs <gmx-users at gromacs.org>; ??? <sunyeping at aliyun.com>
> Subject:Re: [gmx-users] how to include multiple energy groups for
> interaction energy calculation?
>
>
>
> On 1/20/20 7:58 AM, sunyeping wrote:
> > Dear all,
> >
> > I am doing MD simulations on a protein-ligand complex. This complex has
> 4  protein subunits, with each subunits binding one ligand, so there are 4
> ligands (named LIG1, LIG2, LIG3 and LIG4, respectively) in it. I have
> finished the production run and get a trajectory, and now I want to
> calculate the interaction energy between each ligand and their binding
> protein subunit, respectively. I include the  "energygrps" parameter in the
> mdp file for generating a tpr file for rerun the trajectory as following:
> >      energygrps      =  Protein LIG1
> >
> > This seems to work fine. However, could it be possible to include all
> four ligands in the "energygrps" parameter and rerun the trajectory once to
> get the interaction energy between all the four ligands and their
> respective binding protein subunit? I tried to write the "energygrps"
> parameter as following:
> >    energygrps      =  Protein LIG1, Protein LIG2, Protein LIG3, Protein
> LIG4
> > and run the "grompp" command:
> >       gmx grompp -f ie.mdp -c npt.gro -t npt.cpt -p topol.top -n
> index.ndx -o ie.tpr
> > I received the following error:
> >      Fatal error:
> > Group LIG1, referenced in the .mdp file was not found in the index file.
> > Group names must match either [moleculetype] names or custom index group
> > names, in which case you must supply an index file to the '-n' option
> > of grompp.
> >
> > I am sure that LIG1 is included in the index file. This error is most
> probably caused by the incorrect input of the "energygrps" parameter in the
> mdp file.
> >
> > So I wonder whether it is possible to include multiple energy groups in
> the mdp file or I have to rerun the trajectory four times to get the
> interaction energy for the four ligands?
>
> The list of energygrps should not be comma-delimited. You should specify:
>
> energygrps = Protein LIG1 LIG2 LIG3 LIG4
>
> and this will generate a full matrix of interactions among all four
> species. The LIG1-LIG2, LIG1-LIG3, etc. may not be interesting to you
> but this is how you get all of the interaction energies with the protein
> in one shot.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

From alashkov83 at gmail.com  Tue Jan 21 08:20:52 2020
From: alashkov83 at gmail.com (=?UTF-8?B?0JDQu9C10LrRgdCw0L3QtNGAINCb0LDRiNC60L7Qsg==?=)
Date: Tue, 21 Jan 2020 07:20:52 -0000
Subject: [gmx-users] how to include multiple energy groups for
 interaction energy calculation?
In-Reply-To: <CACc8-jxQU+1pVmt7KNsD2GPTvVVJ4AGDuSQpD-YH3hfLZ1JQkQ@mail.gmail.com>
References: <d2374645-1e09-4c7d-aabe-9028643f00f6.sunyeping@aliyun.com>
	<e932d046-f430-acf0-e98c-ef106544384b@vt.edu>
	<047545aa-e2af-46f4-9d2b-0796df0a8c6b.sunyeping@aliyun.com>
	<CACc8-jxQU+1pVmt7KNsD2GPTvVVJ4AGDuSQpD-YH3hfLZ1JQkQ@mail.gmail.com>
Message-ID: <CACc8-jyuLitZqKzxsY2qkQ=Z=bAn4bZ75u5qTH2vUh5u+xS8xw@mail.gmail.com>

*3 valence bond/.

??, 21 ???. 2020 ?. ? 10:19, ????????? ?????? <alashkov83 at gmail.com>:

> This ok. This term show non-bonded interaction for atoms
> located through two valence bonds.
> Alex
>
> ??, 21 ???. 2020 ?. ? 10:06, sunyeping <sunyeping at aliyun.com>:
>
>> Hi Justin,
>>
>> Thank you for reply. "energygrps = Protein LIG1 LIG2 LIG3 LIG4" can do
>> the work. I still have a couple of questions:
>>
>> (1) When using the "gmx energy -f ie.edr -o ie.xvg" to extract the
>> interaction energy, the interested energy terms should be input. Because
>> there are four ligands in my structure, there are accordingly 16 terms, for
>> example, 22 Coul-SR:Protein-LIG1, 23 LJ-SR:Protein-LIG1, 24
>> Coul-14:Protein-LIG1 and 25 LJ-14-LIG1 etc.. I can input the no. of these
>> 16 terms one by one as "22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37",
>> but is there a simple syntax for this selection? I tried "22 to 37" and
>> "22-37", but they doesn't work.
>>
>> (2) I find that the values of  all  Coul-14 and LJ-14 terms are zero.
>> Does this make any sense?
>>
>> Best,
>>
>> Yeping Sun
>> ------------------------------------------------------------------
>> From:Justin Lemkul <jalemkul at vt.edu>
>> Sent At:2020 Jan. 20 (Mon.) 22:17
>> To:gromacs <gmx-users at gromacs.org>; ??? <sunyeping at aliyun.com>
>> Subject:Re: [gmx-users] how to include multiple energy groups for
>> interaction energy calculation?
>>
>>
>>
>> On 1/20/20 7:58 AM, sunyeping wrote:
>> > Dear all,
>> >
>> > I am doing MD simulations on a protein-ligand complex. This complex has
>> 4  protein subunits, with each subunits binding one ligand, so there are 4
>> ligands (named LIG1, LIG2, LIG3 and LIG4, respectively) in it. I have
>> finished the production run and get a trajectory, and now I want to
>> calculate the interaction energy between each ligand and their binding
>> protein subunit, respectively. I include the  "energygrps" parameter in the
>> mdp file for generating a tpr file for rerun the trajectory as following:
>> >      energygrps      =  Protein LIG1
>> >
>> > This seems to work fine. However, could it be possible to include all
>> four ligands in the "energygrps" parameter and rerun the trajectory once to
>> get the interaction energy between all the four ligands and their
>> respective binding protein subunit? I tried to write the "energygrps"
>> parameter as following:
>> >    energygrps      =  Protein LIG1, Protein LIG2, Protein LIG3, Protein
>> LIG4
>> > and run the "grompp" command:
>> >       gmx grompp -f ie.mdp -c npt.gro -t npt.cpt -p topol.top -n
>> index.ndx -o ie.tpr
>> > I received the following error:
>> >      Fatal error:
>> > Group LIG1, referenced in the .mdp file was not found in the index file.
>> > Group names must match either [moleculetype] names or custom index group
>> > names, in which case you must supply an index file to the '-n' option
>> > of grompp.
>> >
>> > I am sure that LIG1 is included in the index file. This error is most
>> probably caused by the incorrect input of the "energygrps" parameter in the
>> mdp file.
>> >
>> > So I wonder whether it is possible to include multiple energy groups in
>> the mdp file or I have to rerun the trajectory four times to get the
>> interaction energy for the four ligands?
>>
>> The list of energygrps should not be comma-delimited. You should specify:
>>
>> energygrps = Protein LIG1 LIG2 LIG3 LIG4
>>
>> and this will generate a full matrix of interactions among all four
>> species. The LIG1-LIG2, LIG1-LIG3, etc. may not be interesting to you
>> but this is how you get all of the interaction energies with the protein
>> in one shot.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>
>

From tdeepanshi248 at gmail.com  Tue Jan 21 08:28:10 2020
From: tdeepanshi248 at gmail.com (Deepanshi .)
Date: Tue, 21 Jan 2020 07:28:10 -0000
Subject: [gmx-users] compressibility values in coarse grained simulations
In-Reply-To: <CAB16xbSrgk718ge2r-v6=fjDzivN1cbOjHo9xiHXO=HZQtqgMg@mail.gmail.com>
References: <CAB16xbSrgk718ge2r-v6=fjDzivN1cbOjHo9xiHXO=HZQtqgMg@mail.gmail.com>
Message-ID: <CAB16xbRMVOQY8RERg1CZx7mK_S1Mf6NdG9LP+3PbU5p2+Q4h9g@mail.gmail.com>

Dear all,

I am using the coarse-grained molecular dynamics simulation to study
membranes. In the production run .mdp file, to control the pressure I am
using semiisotropic in the Pcoupltype option. I wanted to ask how many
values I should give to compressibility and ref_p and what will happen if I
give more or fewer values than the actual values?
Also, I wanted to ask that for coarse-grained simulations the value for
compressibility should be 3e-5 or 4e-5?

Thanks.

Regards,
Deepanshi.

From alessandra.villa.biosim at gmail.com  Tue Jan 21 09:37:00 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Tue, 21 Jan 2020 08:37:00 -0000
Subject: [gmx-users] Uniaxial elongation using deform option
In-Reply-To: <CAMpF9Q0aXLzCxff6fgJt=CTbwnMsWjq_rTf21ohAfx7LO8P1MQ@mail.gmail.com>
References: <CAMpF9Q0aXLzCxff6fgJt=CTbwnMsWjq_rTf21ohAfx7LO8P1MQ@mail.gmail.com>
Message-ID: <CANogp5xFWNYByb-SLceyYLqDK5Mzdep9nehREkfFaeT9x8KZcQ@mail.gmail.com>

Hi,
Some comments below. I hope they help you

On Mon, Jan 20, 2020 at 6:51 AM Pragati Sharma <pragati2325 at gmail.com>
wrote:

> Dear all,
>
> I want to calculate young's modulus of a polymer using uniaxial elongation.
> (elongation in z axis but no volume change)
> I am using 'deform' option and semiisotropic pressure coupling and zero
> compressibility in z for that.

My mdp parameters ar:
>
> *Pcoupl                   = BerendsenPcoupltype            =
> semiisotropictau_p                     = 1compressibility       = 4.5e-5
> 0


compressibility       = 4.5e-5 is  the compressibility for water solution.
Is this value also appropriate for the simulated system?



> ref_p                       = 1 1gen_vel                    = nogen_temp
>               = 298; options for non-eq viscosity calcdeform = 0 0 0.001 0
> 0 0refcoord_scaling = com*
>
>
Do you need refcoord_scaling? See for details
http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=ref%20coord%20scaling#mdp-refcoord-scaling



> Since elongation is in z axis, Lz increases, and Lx and Ly decreases, but
> the decrease in these two axis is less compared to increase in Lz, and so
> my volume is not conserved, it is increasing.
>
>
The simulations are performed using the pressure coupling, thus controlling
the pressure.
I suggest to monitor the pressure along x and y to check if the simulation
setting are appropriate.
Are those values constant and at the desired values?



> Can anyone suggest me some way for uniaxial elongation in gromacs, but
> volume should not change
>
> Thanks!
>

Best regards
Alessandra



> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Tue Jan 21 09:52:14 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Tue, 21 Jan 2020 08:52:14 -0000
Subject: [gmx-users] compressibility values in coarse grained simulations
In-Reply-To: <CAB16xbSrgk718ge2r-v6=fjDzivN1cbOjHo9xiHXO=HZQtqgMg@mail.gmail.com>
References: <CAB16xbSrgk718ge2r-v6=fjDzivN1cbOjHo9xiHXO=HZQtqgMg@mail.gmail.com>
Message-ID: <CANogp5xGrBkSdRh=Txx8WOYtKk6jd+7fKoHWajJSfBbXhf9JBA@mail.gmail.com>

Hi,

On Fri, Jan 3, 2020 at 12:04 PM Deepanshi . <tdeepanshi248 at gmail.com> wrote:

> Dear all,
>
> I am using the coarse-grained molecular dynamics simulation to study
> membranes. In the production run .mdp file, to control the pressure I am
> using semiisotropic in the Pcoupltype option. I wanted to ask how many
> values I should give to compressibility

and ref_p

2 values
(see
http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=semiisotropic#mdp-value-pcoupltype=semiisotropic
)


> and what will happen if I
> give more or fewer values than the actual values?
>

I do not know. But 1) you may get an error when running grompp 2)
you could look at md.log to see what is the taken setting.



> Also, I wanted to ask that for coarse-grained simulations the value for
> compressibility should be 3e-5 or 4e-5?
>

Some CG models (like for example MARTINI) provides  specific setting for
pressure coupling.
If you are using an already developed CG model, I suggest to refer to the
authors suggestions.

Best regards
Alessandra

>
> Thanks.
>
> Regards,
> Deepanshi.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Tue Jan 21 09:53:14 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Tue, 21 Jan 2020 08:53:14 -0000
Subject: [gmx-users] compressibility values in coarse grained simulations
In-Reply-To: <CAB16xbSrgk718ge2r-v6=fjDzivN1cbOjHo9xiHXO=HZQtqgMg@mail.gmail.com>
References: <CAB16xbSrgk718ge2r-v6=fjDzivN1cbOjHo9xiHXO=HZQtqgMg@mail.gmail.com>
Message-ID: <CANogp5xGrBkSdRh=Txx8WOYtKk6jd+7fKoHWajJSfBbXhf9JBA@mail.gmail.com>

Hi,

On Fri, Jan 3, 2020 at 12:04 PM Deepanshi . <tdeepanshi248 at gmail.com> wrote:

> Dear all,
>
> I am using the coarse-grained molecular dynamics simulation to study
> membranes. In the production run .mdp file, to control the pressure I am
> using semiisotropic in the Pcoupltype option. I wanted to ask how many
> values I should give to compressibility

and ref_p

2 values
(see
http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=semiisotropic#mdp-value-pcoupltype=semiisotropic
)


> and what will happen if I
> give more or fewer values than the actual values?
>

I do not know. But 1) you may get an error when running grompp 2)
you could look at md.log to see what is the taken setting.



> Also, I wanted to ask that for coarse-grained simulations the value for
> compressibility should be 3e-5 or 4e-5?
>

Some CG models (like for example MARTINI) provides  specific setting for
pressure coupling.
If you are using an already developed CG model, I suggest to refer to the
authors suggestions.

Best regards
Alessandra

>
> Thanks.
>
> Regards,
> Deepanshi.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From mulpurinagaraju at rediffmail.com  Tue Jan 21 09:58:08 2020
From: mulpurinagaraju at rediffmail.com (Nagaraju Mulpuri)
Date: Tue, 21 Jan 2020 08:58:08 -0000
Subject: [gmx-users] =?utf-8?q?Regarding_Secondary_Structure_Analysis?=
Message-ID: <20200121085120.4747.qmail@f5mail-224-160.rediffmail.com>

Dear Gromacs Users,I am trying to analyse secondary structure of protein. The trajectory generated using Gromacs and protein contains 10 chains. I want to know secondary structural changes, occupancy of each residue in each chain.example (sum on whole trajectory of a chain or protein):&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; residue number: 1 &nbsp; &nbsp;&nbsp;&nbsp;&nbsp;2&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;3&nbsp;&nbsp;&nbsp;&nbsp; 4&nbsp;&nbsp;&nbsp;&nbsp; 5&nbsp;&nbsp;&nbsp;&nbsp; 6&nbsp;&nbsp;&nbsp;&nbsp; 7&nbsp;&nbsp;&nbsp;&nbsp; 8&nbsp;&nbsp;&nbsp;&nbsp; 9&nbsp;&nbsp;&nbsp;&nbsp; 10&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;coil: &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 0.1&nbsp;&nbsp;&nbsp;&nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;&nbsp;helix:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; B-sheet:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;I am trying to use the following command to do secondary structural analysis:&nbsp;gmx do_dssp -f protein.xtc -s protein.gro -n chain_1.ndx -o chain_1.xpm -tu ns -sc chain_scount.xvg?gmx xpm2ps -f chain_1.xpm -o chain_1.psWhen I run above &nbsp;commands on single chain, beta sheets were not shown(chain_1.ps), but when I run on all chains (10 chains) it is showing existence of beta sheets (protein.ps file).&nbsp;&nbsp;At the end of&nbsp;chain_scount.xvg&nbsp;(when using 
 -sc option) file, commented line (# SS %), does it represent percentage of secondary structure?what is meant by chain_separator in legends in scount.xvg file?&nbsp;Any help or suggestions are appreciated.Thank you very much.Sincerely,Nagaraju

From harry.greenblatt at weizmann.ac.il  Tue Jan 21 10:16:05 2020
From: harry.greenblatt at weizmann.ac.il (Harry Mark Greenblatt)
Date: Tue, 21 Jan 2020 09:16:05 -0000
Subject: [gmx-users] domain decomposition failure
Message-ID: <AD0A946B-11FC-4317-9430-B801FAFAB3E7@weizmann.ac.il>

BS?D


Dear All,

  I have now run into this issue with two very different systems (one with 762 protein and 60 DNA residues, the other with 90 protein residues).  If I try and carry over the velocities from the final equilibration step into a production run, and try to use more than one MPI rank, I get an error like

Not all bonded interactions have been properly assigned to the domain decomposition cells
A list of missing interactions:
                Bond of   7320 missing     41
               Angle of  25159 missing    193
         Proper Dih. of  39680 missing    450
       Improper Dih. of   2524 missing     15
               LJ-14 of  35682 missing    286

and the job hangs.

This occurs in Version 2019.4 and 2019.5, and both systems were solvated with water and ions, and neutralised wrt charge.

The only way to proceed is to either:

1.  Run one MPI rank (rather slow)

or

2.  Set
  continuation   = no
  gen_vel    = yes

I presume the desirable thing to do is to carry over the velocities, but that does not seem to work properly.  I can provide more details to the developers, if this appears to be abnormal behaviour.

Thanks


Harry



--------------------------------------------------------------------
Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology           harry.greenblatt at weizmann.ac.il<mailto:harry.greenblatt at weizmann.ac.il>
Weizmann Institute of Science        Phone:  972-8-934-6340
234 Herzl St.                        Facsimile:   972-8-934-3361
Rehovot, 7610001
Israel


From mulpurinagaraju at rediffmail.com  Tue Jan 21 11:13:21 2020
From: mulpurinagaraju at rediffmail.com (Nagaraju Mulpuri)
Date: Tue, 21 Jan 2020 10:13:21 -0000
Subject: [gmx-users] =?utf-8?q?Secondary_Structure_Analysis_using_do=5Fdss?=
	=?utf-8?q?p?=
Message-ID: <20200121100634.16139.qmail@f5mail-224-122.rediffmail.com>

Dear Gromacs Users,&nbsp;I am trying to analyze secondary structure of protein. The trajectory generated using Gromacs and protein contains 10 chains. I want to know secondary structural changes, occupancy of each residue in each chain.&nbsp;example (sum on whole trajectory of a chain or protein):&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; residue number: 1 &nbsp; &nbsp;&nbsp;&nbsp;&nbsp;2&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;3&nbsp;&nbsp;&nbsp;&nbsp; 4&nbsp;&nbsp;&nbsp;&nbsp; 5&nbsp;&nbsp;&nbsp;&nbsp; 6&nbsp;&nbsp;&nbsp;&nbsp; 7&nbsp;&nbsp;&nbsp;&nbsp; 8&nbsp;&nbsp;&nbsp;&nbsp; 9&nbsp;&nbsp;&nbsp;&nbsp; 10&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;coil: &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 0.1&nbsp;&nbsp;&nbsp;&nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;&nbsp;helix:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; B-sheet:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;&nbsp;I am trying to use the following command to do secondary structural analysis:&nbsp;&nbsp;gmx do_dssp -f protein.xtc -s protein.gro -n chain_1.ndx -o chain_1.xpm -tu ns -sc chain_scount.xvg&nbsp;gmx xpm2ps -f chain_1.xpm -o chain_1.ps&nbsp;When I run above &nbsp;commands on single chain, beta sheets were not shown(chain_1.ps), but when I run on all chains (10 chains) it is showing existence of beta sheets (protein.ps file).&nbsp;&nbsp;&nbsp;At the end of&
 nbsp;chain_scount.xvg&nbsp;(when using -sc option) file, commented line (# SS %), does it represent percentage of secondary structure?&nbsp;what is meant by chain_separator in legends in scount.xvg file?&nbsp;&nbsp;Any help or suggestions is appreciated.&nbsp;Thank you very much.&nbsp;Sincerely,Nagaraju&nbsp;

From sadafrani6 at gmail.com  Tue Jan 21 11:31:29 2020
From: sadafrani6 at gmail.com (Sadaf Rani)
Date: Tue, 21 Jan 2020 10:31:29 -0000
Subject: [gmx-users] how to set vdw_lambdas and coul_lambdas
Message-ID: <CAH9Uu9Nirjyv7K-W8ooWm=L+CFUP+-wMDZB-8H2wz5-U_tUgCg@mail.gmail.com>

Dear Gromacs users

I am trying to run a free energy calculation of ligand with protein in
which I am going to transform electrostatics going from lambda 0 to 1 when
vdw interactions and restraints are there, and in the second step
transforming vdw interactions while switching off electrostatics.
The thing which is confusing me is how should I switch off any of the above
parameters should all lambda should be set to 1 or zero? e.g for while
transforming electrostaticss I am setting vdw_lambdas, coul_lambdas
and restraint_lambdas as below:-
vdw_lambdas              = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
coul_lambdas             = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40
0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00
restraint_lambdas        = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00

Is it the right way of doing this?

I need your suggestions, please.

Thanks

Sadaf

From alashkov83 at gmail.com  Tue Jan 21 11:37:51 2020
From: alashkov83 at gmail.com (=?UTF-8?B?0JDQu9C10LrRgdCw0L3QtNGAINCb0LDRiNC60L7Qsg==?=)
Date: Tue, 21 Jan 2020 10:37:51 -0000
Subject: [gmx-users] how to set vdw_lambdas and coul_lambdas
In-Reply-To: <CAH9Uu9Nirjyv7K-W8ooWm=L+CFUP+-wMDZB-8H2wz5-U_tUgCg@mail.gmail.com>
References: <CAH9Uu9Nirjyv7K-W8ooWm=L+CFUP+-wMDZB-8H2wz5-U_tUgCg@mail.gmail.com>
Message-ID: <CACc8-jzfB2292KwhxM5H16mXnO9OTOJ=-git5inHJjGwVvACiA@mail.gmail.com>

Yes, but coul interaction is not needed decrease with this small step.
Alex

??, 21 ???. 2020 ?. ? 13:31, Sadaf Rani <sadafrani6 at gmail.com>:

> Dear Gromacs users
>
> I am trying to run a free energy calculation of ligand with protein in
> which I am going to transform electrostatics going from lambda 0 to 1 when
> vdw interactions and restraints are there, and in the second step
> transforming vdw interactions while switching off electrostatics.
> The thing which is confusing me is how should I switch off any of the above
> parameters should all lambda should be set to 1 or zero? e.g for while
> transforming electrostaticss I am setting vdw_lambdas, coul_lambdas
> and restraint_lambdas as below:-
> vdw_lambdas              = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> coul_lambdas             = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40
> 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00
> restraint_lambdas        = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
> 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
>
> Is it the right way of doing this?
>
> I need your suggestions, please.
>
> Thanks
>
> Sadaf
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From sadafrani6 at gmail.com  Tue Jan 21 14:01:05 2020
From: sadafrani6 at gmail.com (Sadaf Rani)
Date: Tue, 21 Jan 2020 13:01:05 -0000
Subject: [gmx-users] different number of charges and atoms of ligand in free
	energy calculation
Message-ID: <CAH9Uu9NhbO-8BQSieLcTe+o2b+Bbh7GJXmZntcySd+0g449q3A@mail.gmail.com>

Dear Gromacs users
I am simulating the free energy of binding of a ligand with protein using
the dual topology method. I am getting the following message in log file:-

*There are 28 atoms and 29 charges for free energy perturbation*
I have 27 atoms in ligand plus two Na+ ions, It should give an equal number
of atoms and charges as per my understanding.

Could anyone please suggest me where I am committing any mistake? I will be
really thankful.

Thanks in advance.

Sadaf

Ph.D. visiting student
Lancaster University Uk.

From islamshahee at gmail.com  Tue Jan 21 14:06:22 2020
From: islamshahee at gmail.com (SHAHEE ISLAM)
Date: Tue, 21 Jan 2020 13:06:22 -0000
Subject: [gmx-users] question regarding gmx helix orientation
In-Reply-To: <7f421597-0a8a-3b5e-c7e1-94bdceed5bf0@vt.edu>
References: <CAJZ7aT813R6n3nVAh3WBQvU4GgK1f8HVN1S3ZPkvOQV9ZK=8Gw@mail.gmail.com>
	<CANogp5xBCK66cSN5XFjemWErrBA-UQ2Riv=YsZ94FEMSh6ReWw@mail.gmail.com>
	<CAJZ7aT_M=Br7iSvHrggM0ssSPW4z8S6y_PqEhi=tYLxDPHBd3g@mail.gmail.com>
	<CAJZ7aT8LKJmJvVsmU2vwAF3A=ivGbnT7oSaWwWCDHo5Oz8WC1Q@mail.gmail.com>
	<7f421597-0a8a-3b5e-c7e1-94bdceed5bf0@vt.edu>
Message-ID: <CAJZ7aT-fp-9G0d8XVa3eFqEse9KpTvy8HNZ-5F2rneRsk3b-XQ@mail.gmail.com>

hello,
by using gmx gangle, i am trying to calculate the angle between protein and
bilayer,
gmx gangle -f *.xtc -s *.tpr -n *.ndx -g1 vector -g2 plane -group1 -group2.
but the error i am getting is
Number of positions in selection 1 in the first group not divisible by 2
my questions are
1. how can i select the index file so that angle will be calculated between
protein and bilayer.
2. should i mention group name in the gmx gangle calculation command.
the total atoms of protein is 283
and for bilayer it is 9360.

thanking you
shahee

On Sat, Dec 14, 2019 at 6:23 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/13/19 7:06 AM, SHAHEE ISLAM wrote:
> > Yes ,I am using cg model.
>
> Use gmx gangle.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From micpel at kth.se  Tue Jan 21 17:16:54 2020
From: micpel at kth.se (Michele Pellegrino)
Date: Tue, 21 Jan 2020 16:16:54 -0000
Subject: [gmx-users] .dat file from gmx densmap does not match prescribed
	size
Message-ID: <1579623383417.98064@kth.se>

Hello,


I am struggling a little bit with gmx densmap. I am trying to obtain a matrix with density values from the .dat file generated by the program; however the number of data in the output file does not match what I am expecting.

I tried to prescribe both the number of bins in each direction (-n1 and -n2 options) and the grid size (-bin option), not at the same, of course:


gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -n1 4772 -n2 3531


OR (equivalently):


gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -bin 0.01


In both cases I get a dimension mismatch (I expect 16849932 values but I get 4359553).

I am using GROMACS 2019.4?.


What am I doing wrong?


Thanks for your help.


Cheers,

Michele

From marko at kth.se  Tue Jan 21 19:57:14 2020
From: marko at kth.se (Marko Petrovic)
Date: Tue, 21 Jan 2020 18:57:14 -0000
Subject: [gmx-users] Ran into trouble installing Gromacs API
In-Reply-To: <CANMuMvk2faBZdhQMLR8aY4Pa0GZ0G1Wsx8rNZWXKVy3N09w35Q@mail.gmail.com>
References: <mailman.793.1579267153.1966.gromacs.org_gmx-users@maillist.sys.kth.se>
	<CANMuMvk2faBZdhQMLR8aY4Pa0GZ0G1Wsx8rNZWXKVy3N09w35Q@mail.gmail.com>
Message-ID: <D9A1585B-BFE5-4B7D-9740-739E7775A6B9@kth.se>

Thank you

I'll try the other user guide and let you know as soon as I have made a new attempt.

To help me understand documentation navigation issues better, can you tell
me how you ended up at the readthedocs.io<http://readthedocs.io> site while installing GROMACS
2020?
I followed the "Quick start" link from this page:
https://gmxapi.readthedocs.io/en/latest/
And I hoped that it would be gmx2020 compatible.

With Regards
Marko Petrovic
Educator
Computational Science and Technology
School of Electrical Engineering and Computer Science
KTH Royal Institute of Technology

On 20 Jan 2020, at 11:27, Eric Irrgang <ericirrgang at gmail.com<mailto:ericirrgang at gmail.com>> wrote:

Hi Marko,

I'm sorry for the confusion. The install instructions for gmxapi 0.1 on
GROMACS 2020 are at
http://manual.gromacs.org/current/gmxapi/userguide/install.html

I plan to update readthedocs in the next few days to cover both gmxapi
0.0.7 on GROMACS 2019 and gmxapi 0.1 (
https://github.com/kassonlab/gmxapi/issues/249), but I see that the
reorganization of the repository leads to extra confusion (as you describe)
so I will also update the old install docs. (
https://github.com/kassonlab/gmxapi/issues/252)

To help me understand documentation navigation issues better, can you tell
me how you ended up at the readthedocs.io site while installing GROMACS
2020?

From: Marko Petrovic <marko at kth.se>
Subject: [gmx-users] Ran into trouble installing Gromacs API

Hello

I have (I think successfully) installed Gromacs 2020 on my computer (MacOS
X Catalina) and tried to install the API using the quick install guide:
https://gmxapi.readthedocs.io/en/latest/quickstart.html
and get stuck on the step:

pip install -r requirements.txt

as that file does not seem to be in that folder of the repo. I found the
file "requirements-test.txt" in the folder "python-packaging" and tried
with that but got a long error message of missing stuff I didn't
understand, I'm hoping those error messages are from the file not being
intended for use inn the manner I tried so I'm currently not including
those here.

Should I have installed gromacs 2019 for which the API was developed? Has
anyone else installed the API recently and (hopefully) exxperienced and
overcome this hurdle?

With Regards
Marko Petrovic
Educator
Computational Science and Technology
School of Electrical Engineering and Computer Science
KTH Royal Institute of Technology


--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.


From 272699575 at qq.com  Tue Jan 21 21:53:41 2020
From: 272699575 at qq.com (=?gb18030?B?WkhBTkcgQ2hlbmc=?=)
Date: Tue, 21 Jan 2020 20:53:41 -0000
Subject: [gmx-users] Assertion failed for the REMD tutorial
Message-ID: <tencent_03BE88DD2BAF09F099132419153C8F0F5807@qq.com>

I am trying to follow the REMD from Mark Abraham at
http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B


At Stage 2, when I run the grompp command
(for dir in sim[0123]; do cd $dir; gmx grompp -f sim -c confout -t equil-state; cd ..; done)


I got error message:


Program:&nbsp; &nbsp; &nbsp;gmx grompp, version 2019.3
Source file: src/gromacs/fileio/checkpoint.cpp (line 591)
Function:&nbsp; &nbsp; lambda []()-&gt;auto::operator()()-&gt;auto
Assertion failed:
Condition: list != nullptr || (v != nullptr &amp;&amp; vector == nullptr) || (v == nullptr &amp;&amp; vector != nullptr)
Without list, we should have exactly one of v and vector != NULL



The whole log is uploaded at
https://github.com/lanselibai/gromacs-20200121/blob/master/Assertion%20failed.log


Can I ask how to solve this? Thank you!

From 272699575 at qq.com  Tue Jan 21 21:59:46 2020
From: 272699575 at qq.com (=?gb18030?B?WkhBTkcgQ2hlbmc=?=)
Date: Tue, 21 Jan 2020 20:59:46 -0000
Subject: [gmx-users] Assertion failed for the REMD tutorial
Message-ID: <tencent_03BE88DD2BAF09F099132419153C8F0F5807@qq.com>

I am trying to follow the REMD from Mark Abraham at
http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B


At Stage 2, when I run the grompp command
(for dir in sim[0123]; do cd $dir; gmx grompp -f sim -c confout -t equil-state; cd ..; done)


I got error message:


Program:&nbsp; &nbsp; &nbsp;gmx grompp, version 2019.3
Source file: src/gromacs/fileio/checkpoint.cpp (line 591)
Function:&nbsp; &nbsp; lambda []()-&gt;auto::operator()()-&gt;auto
Assertion failed:
Condition: list != nullptr || (v != nullptr &amp;&amp; vector == nullptr) || (v == nullptr &amp;&amp; vector != nullptr)
Without list, we should have exactly one of v and vector != NULL



The whole log is uploaded at
https://github.com/lanselibai/gromacs-20200121/blob/master/Assertion%20failed.log


Can I ask how to solve this? Thank you!

From jalemkul at vt.edu  Tue Jan 21 22:00:04 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Tue, 21 Jan 2020 21:00:04 -0000
Subject: [gmx-users] how to include multiple energy groups for
 interaction energy calculation?
In-Reply-To: <047545aa-e2af-46f4-9d2b-0796df0a8c6b.sunyeping@aliyun.com>
References: <d2374645-1e09-4c7d-aabe-9028643f00f6.sunyeping@aliyun.com>
	<e932d046-f430-acf0-e98c-ef106544384b@vt.edu>
	<047545aa-e2af-46f4-9d2b-0796df0a8c6b.sunyeping@aliyun.com>
Message-ID: <2d27f63c-17ed-e8ee-a426-c244a33f7c6e@vt.edu>



On 1/21/20 2:01 AM, sunyeping wrote:
> Hi Justin,
>
> Thank you for reply. "energygrps?=?Protein?LIG1?LIG2?LIG3?LIG4" can do 
> the work. I still have a couple of questions:
>
> (1) When using the "gmx?energy?-f?ie.edr?-o?ie.xvg" to extract the 
> interaction energy, the interested energy terms should be input. 
> Because there are four ligands in my structure, there are accordingly 
> 16 terms, for example, 22 Coul-SR:Protein-LIG1, 23 LJ-SR:Protein-LIG1, 
> 24 Coul-14:Protein-LIG1 and 25 LJ-14-LIG1 etc.. I can input the no. of 
> these 16 terms one by one as 
> "22?23?24?25?26?27?28?29?30?31?32?33?34?35?36?37", but is there a 
> simple syntax for this selection? I tried "22 to 37" and "22-37", but 
> they doesn't work.
>

You have to enter the groups explicitly and terminate selection with a 0.

> (2) I find that the values of all??Coul-14 and LJ-14 terms are zero. 
> Does this make any sense?
>

Yes, because by definition 1-4 interactions are intramolecular.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From mulpurinagaraju at rediffmail.com  Wed Jan 22 02:17:36 2020
From: mulpurinagaraju at rediffmail.com (Nagaraju Mulpuri)
Date: Wed, 22 Jan 2020 01:17:36 -0000
Subject: [gmx-users] =?utf-8?q?using_do=5Fdssp_secondary_structural_analys?=
	=?utf-8?q?is=2C_beta-sheet_issues?=
Message-ID: <20200122011725.4390.qmail@f5mail-224-152.rediffmail.com>

Dear All,I am trying to analyse secondary structure of protein. The trajectory generated using Gromacs and protein contains 10 chains. I want to know secondary structural changes, occupancy of each residue in each chain.Example(sum on whole trajectory of a chain or protein):residue number &nbsp; &nbsp;1 &nbsp; 2 &nbsp; 3 &nbsp; &nbsp;4 &nbsp; 5 ......10coil &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 0.1 0.1 0.1 0.1 0.1 .... 0.1helix &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 0.1 0.1 0.1 0.1 0.1 .... 0.1sheet &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 0.1 0.1 0.1 0.1 0.1 .... 0.1I &nbsp;am trying to use the following command to do secondary structural analysis:gmx do_dssp -f protein.xtc -s protein.gro -n protein.ndx -o chain_1.xpm -tu ns -sc chain_scount.xvg&nbsp;cmx xpm2ps -f chain_1.xpm -o chain_1.psWhen I run above commands on single chain, beta sheets were not shown (chain_1.ps), but when I ru
 n on all chains (10 chains) it is showing existence of beta sheets.&nbsp;At the end of chain_scount.xvg (when using -sc option) file, commented line(# SS%), does it represents percentage of secondary structure?Any help or suggestions is appreciated.Thank you very much.Sincerely,Nagaraju

From poncho_8629 at hotmail.com  Wed Jan 22 02:31:03 2020
From: poncho_8629 at hotmail.com (Poncho Arvayo Zatarain)
Date: Wed, 22 Jan 2020 01:31:03 -0000
Subject: [gmx-users] Error No Such Moleculetype System
Message-ID: <BN6PR08MB3618FC01A3D8073EA4DFB5FF800C0@BN6PR08MB3618.namprd08.prod.outlook.com>

Hello Gromacs users: im running the following command gmx grompp -p file.top -c solvated.gro -f minimization.mdp -o minimization.tpr but the following error appear: No such Molecule type system (line 16). I know this is about the topology, but i don see nothing strane in line 16. Line 16 is system. I hope can you help me. This is my topology:
#include "martini_v2.2.itp"



#include "Protein_A.itp"
#include "Protein_B.itp"

[ system ]
; name
Martini system from 5iqp.pdb

[ molecules ]
; name        number
Protein_A 1
Protein_B 1
System           1008
Protein          1008
Protein-H        1008
C-alpha          0
Backbone         0
MainChain        0
MainChain+cb     0
MainChain+H      0
SideChain        1008
SideChain+H      1008




From jalemkul at vt.edu  Wed Jan 22 02:33:15 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Wed, 22 Jan 2020 01:33:15 -0000
Subject: [gmx-users] Error No Such Moleculetype System
In-Reply-To: <BN6PR08MB3618FC01A3D8073EA4DFB5FF800C0@BN6PR08MB3618.namprd08.prod.outlook.com>
References: <BN6PR08MB3618FC01A3D8073EA4DFB5FF800C0@BN6PR08MB3618.namprd08.prod.outlook.com>
Message-ID: <707d17a9-20f4-32aa-0188-e34fa799ba93@vt.edu>



On 1/21/20 8:31 PM, Poncho Arvayo Zatarain wrote:
> Hello Gromacs users: im running the following command gmx grompp -p file.top -c solvated.gro -f minimization.mdp -o minimization.tpr but the following error appear: No such Molecule type system (line 16). I know this is about the topology, but i don see nothing strane in line 16. Line 16 is system. I hope can you help me. This is my topology:
> #include "martini_v2.2.itp"
>
>
>
> #include "Protein_A.itp"
> #include "Protein_B.itp"
>
> [ system ]
> ; name
> Martini system from 5iqp.pdb
>
> [ molecules ]
> ; name        number
> Protein_A 1
> Protein_B 1
> System           1008
> Protein          1008
> Protein-H        1008
> C-alpha          0
> Backbone         0
> MainChain        0
> MainChain+cb     0
> MainChain+H      0
> SideChain        1008
> SideChain+H      1008

What you have specified are default index groups, which are not 
[moleculetypes]. The only valid [moleculetype] directives are the ones 
found in the #included .itp files, which likely correspond to Protein_A 
and Protein_B.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From jalemkul at vt.edu  Wed Jan 22 02:34:18 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Wed, 22 Jan 2020 01:34:18 -0000
Subject: [gmx-users] using do_dssp secondary structural analysis,
 beta-sheet issues
In-Reply-To: <20200122011725.4390.qmail@f5mail-224-152.rediffmail.com>
References: <20200122011725.4390.qmail@f5mail-224-152.rediffmail.com>
Message-ID: <fba793ea-c359-b8e2-476b-6075bd9b63d4@vt.edu>



On 1/21/20 8:17 PM, Nagaraju Mulpuri wrote:
> Dear All,I am trying to analyse secondary structure of protein. The trajectory generated using Gromacs and protein contains 10 chains. I want to know secondary structural changes, occupancy of each residue in each chain.Example(sum on whole trajectory of a chain or protein):residue number &nbsp; &nbsp;1 &nbsp; 2 &nbsp; 3 &nbsp; &nbsp;4 &nbsp; 5 ......10coil &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 0.1 0.1 0.1 0.1 0.1 .... 0.1helix &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 0.1 0.1 0.1 0.1 0.1 .... 0.1sheet &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 0.1 0.1 0.1 0.1 0.1 .... 0.1I &nbsp;am trying to use the following command to do secondary structural analysis:gmx do_dssp -f protein.xtc -s protein.gro -n protein.ndx -o chain_1.xpm -tu ns -sc chain_scount.xvg&nbsp;cmx xpm2ps -f chain_1.xpm -o chain_1.psWhen I run above commands on single chain, beta sheets were not shown (chain_1.ps), but when I ru
>   n on all chains (10 chains) it is showing existence of beta sheets.&nbsp;At the end of chain_scount.xvg (when using -sc option) file, commented line(# SS%), does it represents percentage of secondary structure?Any help or suggestions is appreciated.Thank you very much.Sincerely,Nagaraju

If a sheet is composed of multiple chains, you have to include all 
relevant chains in the analysis. DSSP defines secondary structure based 
on hydrogen bonding patterns. If there is no second chain with which the 
first interacts to form a sheet, then DSSP says no sheet exists at all.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================



From miro.astore at gmail.com  Wed Jan 22 10:07:52 2020
From: miro.astore at gmail.com (Miro Astore)
Date: Wed, 22 Jan 2020 09:07:52 -0000
Subject: [gmx-users] top2psf license
Message-ID: <CAL3MGYRtXJ8W-Xt_cW5mDO4MpU_bfxu9JKKJr=Lw_qyXhVTH7A@mail.gmail.com>

Does anyone know what the license is for the top2psf.pl script.

I'd like to modify and distribute it if possible.

Best, Miro.

From alessandra.villa.biosim at gmail.com  Wed Jan 22 10:12:03 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Wed, 22 Jan 2020 09:12:03 -0000
Subject: [gmx-users] Assertion failed for the REMD tutorial
In-Reply-To: <tencent_03BE88DD2BAF09F099132419153C8F0F5807@qq.com>
References: <tencent_03BE88DD2BAF09F099132419153C8F0F5807@qq.com>
Message-ID: <CANogp5yF_B=x-GPsubTdDaO4dYNw5Y7VQH=N=sASFHL17Q3uDQ@mail.gmail.com>

Hi,

On Tue, Jan 21, 2020 at 9:55 PM ZHANG Cheng <272699575 at qq.com> wrote:

> I am trying to follow the REMD from Mark Abraham at
>
> http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B
>
>
>
The tutorial was meant for the GROMACS version 4.6.3. As I can see from the
md.log file, you are using version 2019.3.
As the md.log shows, you have a lot of obsolete mdp entry. Better to update
the mdp entries.
(see
http://manual.gromacs.org/2019-current/user-guide/mdp-options.html#mdp-general
)




> At Stage 2, when I run the grompp command
> (for dir in sim[0123]; do cd $dir; gmx grompp -f sim -c confout -t
> equil-state; cd ..; done)
>
>
> I got error message:
>
>
> Program:&nbsp; &nbsp; &nbsp;gmx grompp, version 2019.3
> Source file: src/gromacs/fileio/checkpoint.cpp (line 591)
> Function:&nbsp; &nbsp; lambda []()-&gt;auto::operator()()-&gt;auto
> Assertion failed:
> Condition: list != nullptr || (v != nullptr &amp;&amp; vector == nullptr)
> || (v == nullptr &amp;&amp; vector != nullptr)
> Without list, we should have exactly one of v and vector != NULL
>
>
>
  md.log reports a problem with the checkpoint file that you provide to
grompp with the option -t (maybe the file was generated with an older
GROMACS version? or for a different system?)

Best regards
Alessandra


>
> The whole log is uploaded at
>
> https://github.com/lanselibai/gromacs-20200121/blob/master/Assertion%20failed.log
>
>
> Can I ask how to solve this? Thank you!
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Wed Jan 22 10:12:04 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Wed, 22 Jan 2020 09:12:04 -0000
Subject: [gmx-users] Assertion failed for the REMD tutorial
In-Reply-To: <tencent_03BE88DD2BAF09F099132419153C8F0F5807@qq.com>
References: <tencent_03BE88DD2BAF09F099132419153C8F0F5807@qq.com>
Message-ID: <CANogp5yF_B=x-GPsubTdDaO4dYNw5Y7VQH=N=sASFHL17Q3uDQ@mail.gmail.com>

Hi,

On Tue, Jan 21, 2020 at 9:55 PM ZHANG Cheng <272699575 at qq.com> wrote:

> I am trying to follow the REMD from Mark Abraham at
>
> http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B
>
>
>
The tutorial was meant for the GROMACS version 4.6.3. As I can see from the
md.log file, you are using version 2019.3.
As the md.log shows, you have a lot of obsolete mdp entry. Better to update
the mdp entries.
(see
http://manual.gromacs.org/2019-current/user-guide/mdp-options.html#mdp-general
)




> At Stage 2, when I run the grompp command
> (for dir in sim[0123]; do cd $dir; gmx grompp -f sim -c confout -t
> equil-state; cd ..; done)
>
>
> I got error message:
>
>
> Program:&nbsp; &nbsp; &nbsp;gmx grompp, version 2019.3
> Source file: src/gromacs/fileio/checkpoint.cpp (line 591)
> Function:&nbsp; &nbsp; lambda []()-&gt;auto::operator()()-&gt;auto
> Assertion failed:
> Condition: list != nullptr || (v != nullptr &amp;&amp; vector == nullptr)
> || (v == nullptr &amp;&amp; vector != nullptr)
> Without list, we should have exactly one of v and vector != NULL
>
>
>
  md.log reports a problem with the checkpoint file that you provide to
grompp with the option -t (maybe the file was generated with an older
GROMACS version? or for a different system?)

Best regards
Alessandra


>
> The whole log is uploaded at
>
> https://github.com/lanselibai/gromacs-20200121/blob/master/Assertion%20failed.log
>
>
> Can I ask how to solve this? Thank you!
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From miro.astore at gmail.com  Wed Jan 22 10:53:10 2020
From: miro.astore at gmail.com (Miro Astore)
Date: Wed, 22 Jan 2020 09:53:10 -0000
Subject: [gmx-users] top2psf license
In-Reply-To: <CAL3MGYRtXJ8W-Xt_cW5mDO4MpU_bfxu9JKKJr=Lw_qyXhVTH7A@mail.gmail.com>
References: <CAL3MGYRtXJ8W-Xt_cW5mDO4MpU_bfxu9JKKJr=Lw_qyXhVTH7A@mail.gmail.com>
Message-ID: <CAL3MGYT_s7-MayLNCHRzaxVVbAcASR7jnk-34Nf_sTf96zkhBg@mail.gmail.com>

I have contacted the author Marc Baaden and he has told me that the script
should be distributed under BDS-3 clause version. Please if you do modify
or distribute this script make sure you copy the license text in the
header.

He's also asked me to share that unity Mol can determine topology and
secondary structures without the need for such a script, directly reading
itp files. Even being able to determine secondary structures from martini.


https://twitter.com/Matth_Chavent/status/1145727900286693376

 Best, Miro

Le mer. 22 janv. 2020 ? 20:07, Miro Astore <miro.astore at gmail.com> a ?crit :

> Does anyone know what the license is for the top2psf.pl script.
>
> I'd like to modify and distribute it if possible.
>
> Best, Miro.
>
>

From sadafrani6 at gmail.com  Wed Jan 22 10:55:05 2020
From: sadafrani6 at gmail.com (Sadaf Rani)
Date: Wed, 22 Jan 2020 09:55:05 -0000
Subject: [gmx-users] Problem of lincs in free energy calculations
Message-ID: <CAH9Uu9NS3nrU8++nZXGK7Z=6ZZ1uQ=Tk=dYbzKPj1m8S5S8jxw@mail.gmail.com>

Dear Gromacs users
During free energy calculation, I am getting lincs warning at MD run in
some of Lambda windows. To cope with this I have reduced my time step to 1
fs rather than 2. Some of them converged but for others, it still gives
lincs warning and generates different PDB structures. If the initial
topology had some issue it should not work for any system.
Could you please suggest me how should I fix this error?

Thanks

Sadaf Rani
Ph.D. visiting student
Lancaster University
United kingdom

From erik.marklund at kemi.uu.se  Wed Jan 22 11:34:53 2020
From: erik.marklund at kemi.uu.se (Erik Marklund)
Date: Wed, 22 Jan 2020 10:34:53 -0000
Subject: [gmx-users] Fourier dihedrals
Message-ID: <C1FA0B22-02D1-443C-8510-4E2158D59289@kemi.uu.se>

Dear all,

I am looking in the manual at how the Fourier dihedrals are defined, and there appears to be a discrepancy between section 5.5 and the table of topology directives in 5.14. 5.5 shows an equation with four coefficients (F1, F2, F3, F4), whereas the table shows 5 coefficients for the Fourier-type dihedrals (C1,C2,C3,C4,C5). How does gromacs actually handle this? With 4 or 5 parameters?

Kind regards,
Erik
______________________________________________
Erik Marklund, PhD, Associate Professor of Biochemistry
Associate Senior Lecturer in Computational Biochemistry
Department of Chemistry ? BMC, Uppsala University
+46 (0)18 471 4562
erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>









N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r det kan du l?sa h?r: http://www.uu.se/om-uu/dataskydd-personuppgifter/

E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

From gmx3 at hotmail.com  Wed Jan 22 16:49:31 2020
From: gmx3 at hotmail.com (Berk Hess)
Date: Wed, 22 Jan 2020 15:49:31 -0000
Subject: [gmx-users] .dat file from gmx densmap does not match
	prescribed	size
In-Reply-To: <1579623383417.98064@kth.se>
References: <1579623383417.98064@kth.se>
Message-ID: <AM6PR0202MB3287F8C82774E45CC9E2C3638E0C0@AM6PR0202MB3287.eurprd02.prod.outlook.com>

How are you counting the elements? Lines with 3531 elements are very long, so they can easily exceed some limit.

/Berk

________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michele Pellegrino <micpel at kth.se>
Sent: Tuesday, January 21, 2020 5:16 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] .dat file from gmx densmap does not match prescribed size

Hello,


I am struggling a little bit with gmx densmap. I am trying to obtain a matrix with density values from the .dat file generated by the program; however the number of data in the output file does not match what I am expecting.

I tried to prescribe both the number of bins in each direction (-n1 and -n2 options) and the grid size (-bin option), not at the same, of course:


gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -n1 4772 -n2 3531


OR (equivalently):


gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -bin 0.01


In both cases I get a dimension mismatch (I expect 16849932 values but I get 4359553).

I am using GROMACS 2019.4?.


What am I doing wrong?


Thanks for your help.


Cheers,

Michele
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

From micpel at kth.se  Wed Jan 22 17:08:16 2020
From: micpel at kth.se (Michele Pellegrino)
Date: Wed, 22 Jan 2020 16:08:16 -0000
Subject: [gmx-users] .dat file from gmx densmap does not
	match	prescribed	size
In-Reply-To: <AM6PR0202MB3287F8C82774E45CC9E2C3638E0C0@AM6PR0202MB3287.eurprd02.prod.outlook.com>
References: <1579623383417.98064@kth.se>,
	<AM6PR0202MB3287F8C82774E45CC9E2C3638E0C0@AM6PR0202MB3287.eurprd02.prod.outlook.com>
Message-ID: <1579709255006.86755@kth.se>


What do you mean by 'element'?

Anyway, part of the issue was in how I was reading the file; with a little modification of the script I reduced the mismatch, but it still persists.
Could it be because GROMACS forces a grid with same meshwith in x and (in my case) z direction, so that the used should impose either -n1 OR -n2 (but not both)? Or maybe the issue is just in the format of the .dat output file?

By the way, the simulation box is 47.72970  x 5.51140 x 35.37240 nanometers (if that may help understanding the issue).

Thanks,
Michele

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Berk Hess <gmx3 at hotmail.com>
Sent: 22 January 2020 16:49
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] .dat file from gmx densmap does not match      prescribed      size

How are you counting the elements? Lines with 3531 elements are very long, so they can easily exceed some limit.

/Berk

________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michele Pellegrino <micpel at kth.se>
Sent: Tuesday, January 21, 2020 5:16 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] .dat file from gmx densmap does not match prescribed size

Hello,


I am struggling a little bit with gmx densmap. I am trying to obtain a matrix with density values from the .dat file generated by the program; however the number of data in the output file does not match what I am expecting.

I tried to prescribe both the number of bins in each direction (-n1 and -n2 options) and the grid size (-bin option), not at the same, of course:


gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -n1 4772 -n2 3531


OR (equivalently):


gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -bin 0.01


In both cases I get a dimension mismatch (I expect 16849932 values but I get 4359553).

I am using GROMACS 2019.4?.


What am I doing wrong?


Thanks for your help.


Cheers,

Michele
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

From 272699575 at qq.com  Wed Jan 22 17:55:09 2020
From: 272699575 at qq.com (=?gb18030?B?WkhBTkcgQ2hlbmc=?=)
Date: Wed, 22 Jan 2020 16:55:09 -0000
Subject: [gmx-users] How to set the temperatures for REMD?
Message-ID: <tencent_F5562F07F0DA13241925BCA78F57BEE6DD07@qq.com>

My purpose of running REMD is to generate sufficient conformation sampling, and try to use them to explain the in vitro data at 65C (338.15K).


I am using the "Temperature generator for REMD-simulations" at http://folding.bmc.uu.se/remd/


I am not sure about the "standard/default" values of several parameters. Can I ask how to determine them?


1) Exchange probability: it should be a value between 0 to 1. The higher of the value I set, the shorter intervals of the temperatures are output.&nbsp;


2) Tolerance: by default it is 1e-4. So I just use it?


3) Lower/Upper temperature limit: As I am interested in 338.15K, should the lower limit set to be 338.15K, while the upper limit as 373.15K (i.e.100C)? Should it be even higher?


4) Constraints in water: Fully flexible?


5) Constraints in the protein: All bonds?


6) Hydrogens in protein: All H? (what does this mean?)


Is there a general rule for the number of temperatures used in the REMD? Please feel free to tell me if there is a guidelines for setting the temperatures.


Thank you!

From gmx3 at hotmail.com  Wed Jan 22 18:34:50 2020
From: gmx3 at hotmail.com (Berk Hess)
Date: Wed, 22 Jan 2020 17:34:50 -0000
Subject: [gmx-users] .dat file from gmx densmap does
	not	match	prescribed	size
In-Reply-To: <1579709255006.86755@kth.se>
References: <1579623383417.98064@kth.se>,
	<AM6PR0202MB3287F8C82774E45CC9E2C3638E0C0@AM6PR0202MB3287.eurprd02.prod.outlook.com>,
	<1579709255006.86755@kth.se>
Message-ID: <AM6PR0202MB3287A902E6955EEA3B99A1068E0C0@AM6PR0202MB3287.eurprd02.prod.outlook.com>

A grid element

I looked at the code and it directly uses n1 and n2 you provide. So I thought that it might be that the code reading the file has a limit on the number of characters on a line.

/Berk

________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michele Pellegrino <micpel at kth.se>
Sent: Wednesday, January 22, 2020 5:07 PM
To: gmx-users at gromacs.org <gmx-users at gromacs.org>
Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed size


What do you mean by 'element'?

Anyway, part of the issue was in how I was reading the file; with a little modification of the script I reduced the mismatch, but it still persists.
Could it be because GROMACS forces a grid with same meshwith in x and (in my case) z direction, so that the used should impose either -n1 OR -n2 (but not both)? Or maybe the issue is just in the format of the .dat output file?

By the way, the simulation box is 47.72970  x 5.51140 x 35.37240 nanometers (if that may help understanding the issue).

Thanks,
Michele

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Berk Hess <gmx3 at hotmail.com>
Sent: 22 January 2020 16:49
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] .dat file from gmx densmap does not match      prescribed      size

How are you counting the elements? Lines with 3531 elements are very long, so they can easily exceed some limit.

/Berk

________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michele Pellegrino <micpel at kth.se>
Sent: Tuesday, January 21, 2020 5:16 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] .dat file from gmx densmap does not match prescribed size

Hello,


I am struggling a little bit with gmx densmap. I am trying to obtain a matrix with density values from the .dat file generated by the program; however the number of data in the output file does not match what I am expecting.

I tried to prescribe both the number of bins in each direction (-n1 and -n2 options) and the grid size (-bin option), not at the same, of course:


gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -n1 4772 -n2 3531


OR (equivalently):


gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -bin 0.01


In both cases I get a dimension mismatch (I expect 16849932 values but I get 4359553).

I am using GROMACS 2019.4?.


What am I doing wrong?


Thanks for your help.


Cheers,

Michele
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

From 272699575 at qq.com  Wed Jan 22 18:36:00 2020
From: 272699575 at qq.com (=?gb18030?B?WkhBTkcgQ2hlbmc=?=)
Date: Wed, 22 Jan 2020 17:36:00 -0000
Subject: [gmx-users] How to run REMD for EM, NVT, NPT and production run?
Message-ID: <tencent_B2F9B476A5BDA2C18D4EB66476F18E3E9E09@qq.com>

I have gone through Mark Abraham's tutorial on REMD http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B


Now I would like to run my own REMD, adjusted from Justin's Lysozyme tutorial (is this correct?)&nbsp;
http://www.mdtutorials.com/gmx/lysozyme/index.html


Can I ask,&nbsp;


1) The normal MD involves EM, NVT, NPT and production run, while the REMD in the tutorial involves Stage 1 of equilibration and Stage 2 of production run. Should I run normal MD for EM and NVT, and run REMD for NPT and production run?&nbsp;


2) How many steps should be used for the "-replex" option in the production run? The REMD tutorial uses 100, is this generally applicable? My protein is ~50 kDa.&nbsp;



Thank you!

From micpel at kth.se  Wed Jan 22 18:44:25 2020
From: micpel at kth.se (Michele Pellegrino)
Date: Wed, 22 Jan 2020 17:44:25 -0000
Subject: [gmx-users] .dat file from gmx densmap
 doestnottmatchtprescribedtsize
In-Reply-To: <AM6PR0202MB3287A902E6955EEA3B99A1068E0C0@AM6PR0202MB3287.eurprd02.prod.outlook.com>
References: <1579623383417.98064@kth.se>,
	<AM6PR0202MB3287F8C82774E45CC9E2C3638E0C0@AM6PR0202MB3287.eurprd02.prod.outlook.com>,
	<1579709255006.86755@kth.se>,
	<AM6PR0202MB3287A902E6955EEA3B99A1068E0C0@AM6PR0202MB3287.eurprd02.prod.outlook.com>
Message-ID: <AM6PR10MB20056D82F0B9971F3150CA1FAE0C0@AM6PR10MB2005.EURPRD10.PROD.OUTLOOK.COM>

Ok, thank you.
I am counting the elements assuming they are in an array organized in a row major fashion.

Scarica Outlook per Android<https://aka.ms/ghei36>
________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Berk Hess <gmx3 at hotmail.com>
Sent: Wednesday, January 22, 2020 6:34:47 PM
To: gmx-users at gromacs.org <gmx-users at gromacs.org>
Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed size

A grid element

I looked at the code and it directly uses n1 and n2 you provide. So I thought that it might be that the code reading the file has a limit on the number of characters on a line.

/Berk

________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michele Pellegrino <micpel at kth.se>
Sent: Wednesday, January 22, 2020 5:07 PM
To: gmx-users at gromacs.org <gmx-users at gromacs.org>
Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed size


What do you mean by 'element'?

Anyway, part of the issue was in how I was reading the file; with a little modification of the script I reduced the mismatch, but it still persists.
Could it be because GROMACS forces a grid with same meshwith in x and (in my case) z direction, so that the used should impose either -n1 OR -n2 (but not both)? Or maybe the issue is just in the format of the .dat output file?

By the way, the simulation box is 47.72970  x 5.51140 x 35.37240 nanometers (if that may help understanding the issue).

Thanks,
Michele

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Berk Hess <gmx3 at hotmail.com>
Sent: 22 January 2020 16:49
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] .dat file from gmx densmap does not match      prescribed      size

How are you counting the elements? Lines with 3531 elements are very long, so they can easily exceed some limit.

/Berk

________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michele Pellegrino <micpel at kth.se>
Sent: Tuesday, January 21, 2020 5:16 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] .dat file from gmx densmap does not match prescribed size

Hello,


I am struggling a little bit with gmx densmap. I am trying to obtain a matrix with density values from the .dat file generated by the program; however the number of data in the output file does not match what I am expecting.

I tried to prescribe both the number of bins in each direction (-n1 and -n2 options) and the grid size (-bin option), not at the same, of course:


gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -n1 4772 -n2 3531


OR (equivalently):


gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -bin 0.01


In both cases I get a dimension mismatch (I expect 16849932 values but I get 4359553).

I am using GROMACS 2019.4?.


What am I doing wrong?


Thanks for your help.


Cheers,

Michele
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

From spoel at xray.bmc.uu.se  Wed Jan 22 22:07:26 2020
From: spoel at xray.bmc.uu.se (David van der Spoel)
Date: Wed, 22 Jan 2020 21:07:26 -0000
Subject: [gmx-users] .dat file from gmx densmap
 doestnottmatchtprescribedtsize
In-Reply-To: <AM6PR10MB20056D82F0B9971F3150CA1FAE0C0@AM6PR10MB2005.EURPRD10.PROD.OUTLOOK.COM>
References: <1579623383417.98064@kth.se>
	<AM6PR0202MB3287F8C82774E45CC9E2C3638E0C0@AM6PR0202MB3287.eurprd02.prod.outlook.com>
	<1579709255006.86755@kth.se>
	<AM6PR0202MB3287A902E6955EEA3B99A1068E0C0@AM6PR0202MB3287.eurprd02.prod.outlook.com>
	<AM6PR10MB20056D82F0B9971F3150CA1FAE0C0@AM6PR10MB2005.EURPRD10.PROD.OUTLOOK.COM>
Message-ID: <51c5242e-0721-464e-6786-f26946f1426b@xray.bmc.uu.se>

Den 2020-01-22 kl. 18:44, skrev Michele Pellegrino:
> Ok, thank you.
> I am counting the elements assuming they are in an array organized in a row major fashion.
have you tried supplying -n1 47 -n2 35 to be able to check manually?

(by the way a resolution of 0.1 Angstrom is unlikely to give you a 
smooth surface)
> 
> Scarica Outlook per Android<https://aka.ms/ghei36>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Berk Hess <gmx3 at hotmail.com>
> Sent: Wednesday, January 22, 2020 6:34:47 PM
> To: gmx-users at gromacs.org <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed size
> 
> A grid element
> 
> I looked at the code and it directly uses n1 and n2 you provide. So I thought that it might be that the code reading the file has a limit on the number of characters on a line.
> 
> /Berk
> 
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michele Pellegrino <micpel at kth.se>
> Sent: Wednesday, January 22, 2020 5:07 PM
> To: gmx-users at gromacs.org <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed size
> 
> 
> What do you mean by 'element'?
> 
> Anyway, part of the issue was in how I was reading the file; with a little modification of the script I reduced the mismatch, but it still persists.
> Could it be because GROMACS forces a grid with same meshwith in x and (in my case) z direction, so that the used should impose either -n1 OR -n2 (but not both)? Or maybe the issue is just in the format of the .dat output file?
> 
> By the way, the simulation box is 47.72970  x 5.51140 x 35.37240 nanometers (if that may help understanding the issue).
> 
> Thanks,
> Michele
> 
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Berk Hess <gmx3 at hotmail.com>
> Sent: 22 January 2020 16:49
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] .dat file from gmx densmap does not match      prescribed      size
> 
> How are you counting the elements? Lines with 3531 elements are very long, so they can easily exceed some limit.
> 
> /Berk
> 
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michele Pellegrino <micpel at kth.se>
> Sent: Tuesday, January 21, 2020 5:16 PM
> To: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] .dat file from gmx densmap does not match prescribed size
> 
> Hello,
> 
> 
> I am struggling a little bit with gmx densmap. I am trying to obtain a matrix with density values from the .dat file generated by the program; however the number of data in the output file does not match what I am expecting.
> 
> I tried to prescribe both the number of bins in each direction (-n1 and -n2 options) and the grid size (-bin option), not at the same, of course:
> 
> 
> gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -n1 4772 -n2 3531
> 
> 
> OR (equivalently):
> 
> 
> gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -bin 0.01
> 
> 
> In both cases I get a dimension mismatch (I expect 16849932 values but I get 4359553).
> 
> I am using GROMACS 2019.4?.
> 
> 
> What am I doing wrong?
> 
> 
> Thanks for your help.
> 
> 
> Cheers,
> 
> Michele
> --
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> 


-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se

From micpel at kth.se  Wed Jan 22 22:45:30 2020
From: micpel at kth.se (Michele Pellegrino)
Date: Wed, 22 Jan 2020 21:45:30 -0000
Subject: [gmx-users] .dat file from gmx densmap
 doestnottmatchtprescribedtsize
In-Reply-To: <51c5242e-0721-464e-6786-f26946f1426b@xray.bmc.uu.se>
References: <1579623383417.98064@kth.se>
	<AM6PR0202MB3287F8C82774E45CC9E2C3638E0C0@AM6PR0202MB3287.eurprd02.prod.outlook.com>
	<1579709255006.86755@kth.se>
	<AM6PR0202MB3287A902E6955EEA3B99A1068E0C0@AM6PR0202MB3287.eurprd02.prod.outlook.com>
	<AM6PR10MB20056D82F0B9971F3150CA1FAE0C0@AM6PR10MB2005.EURPRD10.PROD.OUTLOOK.COM>,
	<51c5242e-0721-464e-6786-f26946f1426b@xray.bmc.uu.se>
Message-ID: <1579729527260.17842@kth.se>

I will try, thank you for the tip.
To be fair, this issue came up also when trying to set a meshwidth larger than the one GROMACS prescribes by default (I was trying 0.05 nm instead of 0.02 nm).

Cheers,
Michele
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of David van der Spoel <spoel at xray.bmc.uu.se>
Sent: 22 January 2020 22:07
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize

Den 2020-01-22 kl. 18:44, skrev Michele Pellegrino:
> Ok, thank you.
> I am counting the elements assuming they are in an array organized in a row major fashion.
have you tried supplying -n1 47 -n2 35 to be able to check manually?

(by the way a resolution of 0.1 Angstrom is unlikely to give you a
smooth surface)
>
> Scarica Outlook per Android<https://aka.ms/ghei36>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Berk Hess <gmx3 at hotmail.com>
> Sent: Wednesday, January 22, 2020 6:34:47 PM
> To: gmx-users at gromacs.org <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed size
>
> A grid element
>
> I looked at the code and it directly uses n1 and n2 you provide. So I thought that it might be that the code reading the file has a limit on the number of characters on a line.
>
> /Berk
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michele Pellegrino <micpel at kth.se>
> Sent: Wednesday, January 22, 2020 5:07 PM
> To: gmx-users at gromacs.org <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed size
>
>
> What do you mean by 'element'?
>
> Anyway, part of the issue was in how I was reading the file; with a little modification of the script I reduced the mismatch, but it still persists.
> Could it be because GROMACS forces a grid with same meshwith in x and (in my case) z direction, so that the used should impose either -n1 OR -n2 (but not both)? Or maybe the issue is just in the format of the .dat output file?
>
> By the way, the simulation box is 47.72970  x 5.51140 x 35.37240 nanometers (if that may help understanding the issue).
>
> Thanks,
> Michele
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Berk Hess <gmx3 at hotmail.com>
> Sent: 22 January 2020 16:49
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] .dat file from gmx densmap does not match      prescribed      size
>
> How are you counting the elements? Lines with 3531 elements are very long, so they can easily exceed some limit.
>
> /Berk
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michele Pellegrino <micpel at kth.se>
> Sent: Tuesday, January 21, 2020 5:16 PM
> To: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] .dat file from gmx densmap does not match prescribed size
>
> Hello,
>
>
> I am struggling a little bit with gmx densmap. I am trying to obtain a matrix with density values from the .dat file generated by the program; however the number of data in the output file does not match what I am expecting.
>
> I tried to prescribe both the number of bins in each direction (-n1 and -n2 options) and the grid size (-bin option), not at the same, of course:
>
>
> gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -n1 4772 -n2 3531
>
>
> OR (equivalently):
>
>
> gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -bin 0.01
>
>
> In both cases I get a dimension mismatch (I expect 16849932 values but I get 4359553).
>
> I am using GROMACS 2019.4?.
>
>
> What am I doing wrong?
>
>
> Thanks for your help.
>
>
> Cheers,
>
> Michele
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>


--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

From micpel at kth.se  Wed Jan 22 22:59:27 2020
From: micpel at kth.se (Michele Pellegrino)
Date: Wed, 22 Jan 2020 21:59:27 -0000
Subject: [gmx-users] .dat file from gmx densmap
 doestnottmatchtprescribedtsize
In-Reply-To: <51c5242e-0721-464e-6786-f26946f1426b@xray.bmc.uu.se>
References: <1579623383417.98064@kth.se>
	<AM6PR0202MB3287F8C82774E45CC9E2C3638E0C0@AM6PR0202MB3287.eurprd02.prod.outlook.com>
	<1579709255006.86755@kth.se>
	<AM6PR0202MB3287A902E6955EEA3B99A1068E0C0@AM6PR0202MB3287.eurprd02.prod.outlook.com>
	<AM6PR10MB20056D82F0B9971F3150CA1FAE0C0@AM6PR10MB2005.EURPRD10.PROD.OUTLOOK.COM>,
	<51c5242e-0721-464e-6786-f26946f1426b@xray.bmc.uu.se>
Message-ID: <1579730306553.39210@kth.se>

I tried just now: it did not work: 1728 values expected, 1645 values in the .dat file.
I managed to make it work by defining the number of values in each direction as (in Python):
Nx = np.sqrt(Nda*Lx/Lz)
Nz = Nx*Lz/Lx
Nx = int( np.round(Nx) )
Nz = int( np.round(Nz) )
being Nda the number of values in the .dat file and Lx (resp. Lz) the lenght of the simulation box in the x (z) direction (np stands for numpy).
However, I believe this manipulation should not be necessary.

Cheers,
Michele
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of David van der Spoel <spoel at xray.bmc.uu.se>
Sent: 22 January 2020 22:07
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize

Den 2020-01-22 kl. 18:44, skrev Michele Pellegrino:
> Ok, thank you.
> I am counting the elements assuming they are in an array organized in a row major fashion.
have you tried supplying -n1 47 -n2 35 to be able to check manually?

(by the way a resolution of 0.1 Angstrom is unlikely to give you a
smooth surface)
>
> Scarica Outlook per Android<https://aka.ms/ghei36>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Berk Hess <gmx3 at hotmail.com>
> Sent: Wednesday, January 22, 2020 6:34:47 PM
> To: gmx-users at gromacs.org <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed size
>
> A grid element
>
> I looked at the code and it directly uses n1 and n2 you provide. So I thought that it might be that the code reading the file has a limit on the number of characters on a line.
>
> /Berk
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michele Pellegrino <micpel at kth.se>
> Sent: Wednesday, January 22, 2020 5:07 PM
> To: gmx-users at gromacs.org <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed size
>
>
> What do you mean by 'element'?
>
> Anyway, part of the issue was in how I was reading the file; with a little modification of the script I reduced the mismatch, but it still persists.
> Could it be because GROMACS forces a grid with same meshwith in x and (in my case) z direction, so that the used should impose either -n1 OR -n2 (but not both)? Or maybe the issue is just in the format of the .dat output file?
>
> By the way, the simulation box is 47.72970  x 5.51140 x 35.37240 nanometers (if that may help understanding the issue).
>
> Thanks,
> Michele
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Berk Hess <gmx3 at hotmail.com>
> Sent: 22 January 2020 16:49
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] .dat file from gmx densmap does not match      prescribed      size
>
> How are you counting the elements? Lines with 3531 elements are very long, so they can easily exceed some limit.
>
> /Berk
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michele Pellegrino <micpel at kth.se>
> Sent: Tuesday, January 21, 2020 5:16 PM
> To: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] .dat file from gmx densmap does not match prescribed size
>
> Hello,
>
>
> I am struggling a little bit with gmx densmap. I am trying to obtain a matrix with density values from the .dat file generated by the program; however the number of data in the output file does not match what I am expecting.
>
> I tried to prescribe both the number of bins in each direction (-n1 and -n2 options) and the grid size (-bin option), not at the same, of course:
>
>
> gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -n1 4772 -n2 3531
>
>
> OR (equivalently):
>
>
> gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -bin 0.01
>
>
> In both cases I get a dimension mismatch (I expect 16849932 values but I get 4359553).
>
> I am using GROMACS 2019.4?.
>
>
> What am I doing wrong?
>
>
> Thanks for your help.
>
>
> Cheers,
>
> Michele
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>


--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

From alashkov83 at gmail.com  Thu Jan 23 07:06:15 2020
From: alashkov83 at gmail.com (=?UTF-8?B?0JDQu9C10LrRgdCw0L3QtNGAINCb0LDRiNC60L7Qsg==?=)
Date: Thu, 23 Jan 2020 06:06:15 -0000
Subject: [gmx-users] Problem of lincs in free energy calculations
In-Reply-To: <CAH9Uu9NS3nrU8++nZXGK7Z=6ZZ1uQ=Tk=dYbzKPj1m8S5S8jxw@mail.gmail.com>
References: <CAH9Uu9NS3nrU8++nZXGK7Z=6ZZ1uQ=Tk=dYbzKPj1m8S5S8jxw@mail.gmail.com>
Message-ID: <CACc8-jyWUoE+ccoWscSXJ6GCFq36FE5YRbOkS55=KuDefcc8EQ@mail.gmail.com>

Usually, in this case, Lincs algorithm is not the cause of unstable MD
simulation. It is symptome of possible blowing up. Possible reasons are
described here http://www.gromacs.org/Documentation/Terminology/Blowing_Up
Alex

??, 22 ???. 2020 ?. ? 12:57, Sadaf Rani <sadafrani6 at gmail.com>:

> Dear Gromacs users
> During free energy calculation, I am getting lincs warning at MD run in
> some of Lambda windows. To cope with this I have reduced my time step to 1
> fs rather than 2. Some of them converged but for others, it still gives
> lincs warning and generates different PDB structures. If the initial
> topology had some issue it should not work for any system.
> Could you please suggest me how should I fix this error?
>
> Thanks
>
> Sadaf Rani
> Ph.D. visiting student
> Lancaster University
> United kingdom
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Thu Jan 23 08:47:55 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Thu, 23 Jan 2020 07:47:55 -0000
Subject: [gmx-users] How to set the temperatures for REMD?
In-Reply-To: <tencent_F5562F07F0DA13241925BCA78F57BEE6DD07@qq.com>
References: <tencent_F5562F07F0DA13241925BCA78F57BEE6DD07@qq.com>
Message-ID: <CANogp5wkvn4ZJg7TdHDE209RWr0e-g+jSHyxjkxgRKe1i_+oVA@mail.gmail.com>

Hi,


On Wed, Jan 22, 2020 at 5:55 PM ZHANG Cheng <272699575 at qq.com> wrote:

> My purpose of running REMD is to generate sufficient conformation
> sampling, and try to use them to explain the in vitro data at 65C (338.15K).
>
>
> I am using the "Temperature generator for REMD-simulations" at
> http://folding.bmc.uu.se/remd/
>
>
> I am not sure about the "standard/default" values of several parameters.
> Can I ask how to determine them?
>
>
> 1) Exchange probability: it should be a value between 0 to 1. The higher
> of the value I set, the shorter intervals of the temperatures are
> output.&nbsp;
>
>
>
For the definition of exchange probability (isobaric and isothermal
ensemble) between 2 replicas i and j see eq 4 in
http://manual.gromacs.org/documentation/2019-current/reference-manual/algorithms/replica-exchange.html?highlight=replica%20exchange

Best regards
Alessandra


> 2) Tolerance: by default it is 1e-4. So I just use it?
>
>
> 3) Lower/Upper temperature limit: As I am interested in 338.15K, should
> the lower limit set to be 338.15K, while the upper limit as 373.15K
> (i.e.100C)? Should it be even higher?
>
>
> 4) Constraints in water: Fully flexible?
>
>
> 5) Constraints in the protein: All bonds?
>
>
> 6) Hydrogens in protein: All H? (what does this mean?)
>
>
> Is there a general rule for the number of temperatures used in the REMD?
> Please feel free to tell me if there is a guidelines for setting the
> temperatures.
>
>
> Thank you!
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Thu Jan 23 08:47:55 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Thu, 23 Jan 2020 07:47:55 -0000
Subject: [gmx-users] How to set the temperatures for REMD?
In-Reply-To: <tencent_F5562F07F0DA13241925BCA78F57BEE6DD07@qq.com>
References: <tencent_F5562F07F0DA13241925BCA78F57BEE6DD07@qq.com>
Message-ID: <CANogp5wkvn4ZJg7TdHDE209RWr0e-g+jSHyxjkxgRKe1i_+oVA@mail.gmail.com>

Hi,


On Wed, Jan 22, 2020 at 5:55 PM ZHANG Cheng <272699575 at qq.com> wrote:

> My purpose of running REMD is to generate sufficient conformation
> sampling, and try to use them to explain the in vitro data at 65C (338.15K).
>
>
> I am using the "Temperature generator for REMD-simulations" at
> http://folding.bmc.uu.se/remd/
>
>
> I am not sure about the "standard/default" values of several parameters.
> Can I ask how to determine them?
>
>
> 1) Exchange probability: it should be a value between 0 to 1. The higher
> of the value I set, the shorter intervals of the temperatures are
> output.&nbsp;
>
>
>
For the definition of exchange probability (isobaric and isothermal
ensemble) between 2 replicas i and j see eq 4 in
http://manual.gromacs.org/documentation/2019-current/reference-manual/algorithms/replica-exchange.html?highlight=replica%20exchange

Best regards
Alessandra


> 2) Tolerance: by default it is 1e-4. So I just use it?
>
>
> 3) Lower/Upper temperature limit: As I am interested in 338.15K, should
> the lower limit set to be 338.15K, while the upper limit as 373.15K
> (i.e.100C)? Should it be even higher?
>
>
> 4) Constraints in water: Fully flexible?
>
>
> 5) Constraints in the protein: All bonds?
>
>
> 6) Hydrogens in protein: All H? (what does this mean?)
>
>
> Is there a general rule for the number of temperatures used in the REMD?
> Please feel free to tell me if there is a guidelines for setting the
> temperatures.
>
>
> Thank you!
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From micpel at kth.se  Thu Jan 23 11:02:31 2020
From: micpel at kth.se (Michele Pellegrino)
Date: Thu, 23 Jan 2020 10:02:31 -0000
Subject: [gmx-users] .dat file from gmx densmap
 doestnottmatchtprescribedtsize
In-Reply-To: <1579730306553.39210@kth.se>
References: <1579623383417.98064@kth.se>
	<AM6PR0202MB3287F8C82774E45CC9E2C3638E0C0@AM6PR0202MB3287.eurprd02.prod.outlook.com>
	<1579709255006.86755@kth.se>
	<AM6PR0202MB3287A902E6955EEA3B99A1068E0C0@AM6PR0202MB3287.eurprd02.prod.outlook.com>
	<AM6PR10MB20056D82F0B9971F3150CA1FAE0C0@AM6PR10MB2005.EURPRD10.PROD.OUTLOOK.COM>,
	<51c5242e-0721-464e-6786-f26946f1426b@xray.bmc.uu.se>,
	<1579730306553.39210@kth.se>
Message-ID: <1579773748127.92047@kth.se>

Ok, I believe I have found the nature of this 'quirk' looking at the source code (as Berk suggested me to do).
I was assuming a format, but GROMACS is producing another: the .dat file in the output contains the values PLUS the coordinates for each bin, that is the first row and the first colum are not denisty values, but coordinates; hence the output matrix is indeed (n1+1)x(n2+1), the actual values being in grid[1:n1-1,2:n2-2] (0-start index convention).
So apparently is not a bug in the code, but just a misunderstanding of me as user; I double checked the documentation (both for 2019.04 and for the new 2020 release) and I did not find any reference to the format of the output file: could it be a good idea to incude some indication in that regard?

Cheers,
Michele
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michele Pellegrino <micpel at kth.se>
Sent: 22 January 2020 22:58
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize

I tried just now: it did not work: 1728 values expected, 1645 values in the .dat file.
I managed to make it work by defining the number of values in each direction as (in Python):
Nx = np.sqrt(Nda*Lx/Lz)
Nz = Nx*Lz/Lx
Nx = int( np.round(Nx) )
Nz = int( np.round(Nz) )
being Nda the number of values in the .dat file and Lx (resp. Lz) the lenght of the simulation box in the x (z) direction (np stands for numpy).
However, I believe this manipulation should not be necessary.

Cheers,
Michele
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of David van der Spoel <spoel at xray.bmc.uu.se>
Sent: 22 January 2020 22:07
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize

Den 2020-01-22 kl. 18:44, skrev Michele Pellegrino:
> Ok, thank you.
> I am counting the elements assuming they are in an array organized in a row major fashion.
have you tried supplying -n1 47 -n2 35 to be able to check manually?

(by the way a resolution of 0.1 Angstrom is unlikely to give you a
smooth surface)
>
> Scarica Outlook per Android<https://aka.ms/ghei36>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Berk Hess <gmx3 at hotmail.com>
> Sent: Wednesday, January 22, 2020 6:34:47 PM
> To: gmx-users at gromacs.org <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed size
>
> A grid element
>
> I looked at the code and it directly uses n1 and n2 you provide. So I thought that it might be that the code reading the file has a limit on the number of characters on a line.
>
> /Berk
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michele Pellegrino <micpel at kth.se>
> Sent: Wednesday, January 22, 2020 5:07 PM
> To: gmx-users at gromacs.org <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed size
>
>
> What do you mean by 'element'?
>
> Anyway, part of the issue was in how I was reading the file; with a little modification of the script I reduced the mismatch, but it still persists.
> Could it be because GROMACS forces a grid with same meshwith in x and (in my case) z direction, so that the used should impose either -n1 OR -n2 (but not both)? Or maybe the issue is just in the format of the .dat output file?
>
> By the way, the simulation box is 47.72970  x 5.51140 x 35.37240 nanometers (if that may help understanding the issue).
>
> Thanks,
> Michele
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Berk Hess <gmx3 at hotmail.com>
> Sent: 22 January 2020 16:49
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] .dat file from gmx densmap does not match      prescribed      size
>
> How are you counting the elements? Lines with 3531 elements are very long, so they can easily exceed some limit.
>
> /Berk
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michele Pellegrino <micpel at kth.se>
> Sent: Tuesday, January 21, 2020 5:16 PM
> To: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] .dat file from gmx densmap does not match prescribed size
>
> Hello,
>
>
> I am struggling a little bit with gmx densmap. I am trying to obtain a matrix with density values from the .dat file generated by the program; however the number of data in the output file does not match what I am expecting.
>
> I tried to prescribe both the number of bins in each direction (-n1 and -n2 options) and the grid size (-bin option), not at the same, of course:
>
>
> gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -n1 4772 -n2 3531
>
>
> OR (equivalently):
>
>
> gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -bin 0.01
>
>
> In both cases I get a dimension mismatch (I expect 16849932 values but I get 4359553).
>
> I am using GROMACS 2019.4?.
>
>
> What am I doing wrong?
>
>
> Thanks for your help.
>
>
> Cheers,
>
> Michele
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>


--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

From micpel at kth.se  Thu Jan 23 11:03:58 2020
From: micpel at kth.se (Michele Pellegrino)
Date: Thu, 23 Jan 2020 10:03:58 -0000
Subject: [gmx-users] .dat file from gmx densmap
 doestnottmatchtprescribedtsize
In-Reply-To: <1579730306553.39210@kth.se>
References: <1579623383417.98064@kth.se>
	<AM6PR0202MB3287F8C82774E45CC9E2C3638E0C0@AM6PR0202MB3287.eurprd02.prod.outlook.com>
	<1579709255006.86755@kth.se>
	<AM6PR0202MB3287A902E6955EEA3B99A1068E0C0@AM6PR0202MB3287.eurprd02.prod.outlook.com>
	<AM6PR10MB20056D82F0B9971F3150CA1FAE0C0@AM6PR10MB2005.EURPRD10.PROD.OUTLOOK.COM>,
	<51c5242e-0721-464e-6786-f26946f1426b@xray.bmc.uu.se>,
	<1579730306553.39210@kth.se>
Message-ID: <1579773835944.5857@kth.se>

Ok, I believe I have found the nature of this 'quirk' looking at the source code (as Berk suggested me to do).
I was assuming a format, but GROMACS is producing another: the .dat file in the output contains the values PLUS the coordinates for each bin, that is the first row and the first colum are not denisty values, but coordinates; hence the output matrix is indeed (n1+1)x(n2+1), the actual values being in grid[1:n1-1,1:n2-1] (0-start index convention).
So apparently is not a bug in the code, but just a misunderstanding of me as user; I double checked the documentation (both for 2019.04 and for the new 2020 release) and I did not find any reference to the format of the output file: could it be a good idea to incude some indication in that regard?

Cheers,
Michele

* there is a typo in the original message (2:n2-2 instead of 1:n2-1)
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michele Pellegrino <micpel at kth.se>
Sent: 22 January 2020 22:58
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize

I tried just now: it did not work: 1728 values expected, 1645 values in the .dat file.
I managed to make it work by defining the number of values in each direction as (in Python):
Nx = np.sqrt(Nda*Lx/Lz)
Nz = Nx*Lz/Lx
Nx = int( np.round(Nx) )
Nz = int( np.round(Nz) )
being Nda the number of values in the .dat file and Lx (resp. Lz) the lenght of the simulation box in the x (z) direction (np stands for numpy).
However, I believe this manipulation should not be necessary.

Cheers,
Michele
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of David van der Spoel <spoel at xray.bmc.uu.se>
Sent: 22 January 2020 22:07
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize

Den 2020-01-22 kl. 18:44, skrev Michele Pellegrino:
> Ok, thank you.
> I am counting the elements assuming they are in an array organized in a row major fashion.
have you tried supplying -n1 47 -n2 35 to be able to check manually?

(by the way a resolution of 0.1 Angstrom is unlikely to give you a
smooth surface)
>
> Scarica Outlook per Android<https://aka.ms/ghei36>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Berk Hess <gmx3 at hotmail.com>
> Sent: Wednesday, January 22, 2020 6:34:47 PM
> To: gmx-users at gromacs.org <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed size
>
> A grid element
>
> I looked at the code and it directly uses n1 and n2 you provide. So I thought that it might be that the code reading the file has a limit on the number of characters on a line.
>
> /Berk
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michele Pellegrino <micpel at kth.se>
> Sent: Wednesday, January 22, 2020 5:07 PM
> To: gmx-users at gromacs.org <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed size
>
>
> What do you mean by 'element'?
>
> Anyway, part of the issue was in how I was reading the file; with a little modification of the script I reduced the mismatch, but it still persists.
> Could it be because GROMACS forces a grid with same meshwith in x and (in my case) z direction, so that the used should impose either -n1 OR -n2 (but not both)? Or maybe the issue is just in the format of the .dat output file?
>
> By the way, the simulation box is 47.72970  x 5.51140 x 35.37240 nanometers (if that may help understanding the issue).
>
> Thanks,
> Michele
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Berk Hess <gmx3 at hotmail.com>
> Sent: 22 January 2020 16:49
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] .dat file from gmx densmap does not match      prescribed      size
>
> How are you counting the elements? Lines with 3531 elements are very long, so they can easily exceed some limit.
>
> /Berk
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michele Pellegrino <micpel at kth.se>
> Sent: Tuesday, January 21, 2020 5:16 PM
> To: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] .dat file from gmx densmap does not match prescribed size
>
> Hello,
>
>
> I am struggling a little bit with gmx densmap. I am trying to obtain a matrix with density values from the .dat file generated by the program; however the number of data in the output file does not match what I am expecting.
>
> I tried to prescribe both the number of bins in each direction (-n1 and -n2 options) and the grid size (-bin option), not at the same, of course:
>
>
> gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -n1 4772 -n2 3531
>
>
> OR (equivalently):
>
>
> gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -bin 0.01
>
>
> In both cases I get a dimension mismatch (I expect 16849932 values but I get 4359553).
>
> I am using GROMACS 2019.4?.
>
>
> What am I doing wrong?
>
>
> Thanks for your help.
>
>
> Cheers,
>
> Michele
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>


--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

From blau at kth.se  Thu Jan 23 13:30:11 2020
From: blau at kth.se (Christian Blau)
Date: Thu, 23 Jan 2020 12:30:11 -0000
Subject: [gmx-users] .dat file from gmx densmap
 doestnottmatchtprescribedtsize
In-Reply-To: <1579773835944.5857@kth.se>
References: <1579623383417.98064@kth.se>
	<AM6PR0202MB3287F8C82774E45CC9E2C3638E0C0@AM6PR0202MB3287.eurprd02.prod.outlook.com>
	<1579709255006.86755@kth.se>
	<AM6PR0202MB3287A902E6955EEA3B99A1068E0C0@AM6PR0202MB3287.eurprd02.prod.outlook.com>
	<AM6PR10MB20056D82F0B9971F3150CA1FAE0C0@AM6PR10MB2005.EURPRD10.PROD.OUTLOOK.COM>
	<51c5242e-0721-464e-6786-f26946f1426b@xray.bmc.uu.se>
	<1579730306553.39210@kth.se> <1579773835944.5857@kth.se>
Message-ID: <b90830a2-8d52-89a4-42d0-2658f179139a@kth.se>

Hi Michele,


Thanks for the input and suggestion!


I created a redmine issue using your observations that you can follow at 
https://redmine.gromacs.org/issues/3353


Best,

Christian

On 2020-01-23 11:03, Michele Pellegrino wrote:
> Ok, I believe I have found the nature of this 'quirk' looking at the source code (as Berk suggested me to do).
> I was assuming a format, but GROMACS is producing another: the .dat file in the output contains the values PLUS the coordinates for each bin, that is the first row and the first colum are not denisty values, but coordinates; hence the output matrix is indeed (n1+1)x(n2+1), the actual values being in grid[1:n1-1,1:n2-1] (0-start index convention).
> So apparently is not a bug in the code, but just a misunderstanding of me as user; I double checked the documentation (both for 2019.04 and for the new 2020 release) and I did not find any reference to the format of the output file: could it be a good idea to incude some indication in that regard?
>
> Cheers,
> Michele
>
> * there is a typo in the original message (2:n2-2 instead of 1:n2-1)
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michele Pellegrino <micpel at kth.se>
> Sent: 22 January 2020 22:58
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize
>
> I tried just now: it did not work: 1728 values expected, 1645 values in the .dat file.
> I managed to make it work by defining the number of values in each direction as (in Python):
> Nx = np.sqrt(Nda*Lx/Lz)
> Nz = Nx*Lz/Lx
> Nx = int( np.round(Nx) )
> Nz = int( np.round(Nz) )
> being Nda the number of values in the .dat file and Lx (resp. Lz) the lenght of the simulation box in the x (z) direction (np stands for numpy).
> However, I believe this manipulation should not be necessary.
>
> Cheers,
> Michele
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of David van der Spoel <spoel at xray.bmc.uu.se>
> Sent: 22 January 2020 22:07
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize
>
> Den 2020-01-22 kl. 18:44, skrev Michele Pellegrino:
>> Ok, thank you.
>> I am counting the elements assuming they are in an array organized in a row major fashion.
> have you tried supplying -n1 47 -n2 35 to be able to check manually?
>
> (by the way a resolution of 0.1 Angstrom is unlikely to give you a
> smooth surface)
>> Scarica Outlook per Android<https://aka.ms/ghei36>
>> ________________________________
>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Berk Hess <gmx3 at hotmail.com>
>> Sent: Wednesday, January 22, 2020 6:34:47 PM
>> To: gmx-users at gromacs.org <gmx-users at gromacs.org>
>> Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed size
>>
>> A grid element
>>
>> I looked at the code and it directly uses n1 and n2 you provide. So I thought that it might be that the code reading the file has a limit on the number of characters on a line.
>>
>> /Berk
>>
>> ________________________________
>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michele Pellegrino <micpel at kth.se>
>> Sent: Wednesday, January 22, 2020 5:07 PM
>> To: gmx-users at gromacs.org <gmx-users at gromacs.org>
>> Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed size
>>
>>
>> What do you mean by 'element'?
>>
>> Anyway, part of the issue was in how I was reading the file; with a little modification of the script I reduced the mismatch, but it still persists.
>> Could it be because GROMACS forces a grid with same meshwith in x and (in my case) z direction, so that the used should impose either -n1 OR -n2 (but not both)? Or maybe the issue is just in the format of the .dat output file?
>>
>> By the way, the simulation box is 47.72970  x 5.51140 x 35.37240 nanometers (if that may help understanding the issue).
>>
>> Thanks,
>> Michele
>>
>> ________________________________________
>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Berk Hess <gmx3 at hotmail.com>
>> Sent: 22 January 2020 16:49
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] .dat file from gmx densmap does not match      prescribed      size
>>
>> How are you counting the elements? Lines with 3531 elements are very long, so they can easily exceed some limit.
>>
>> /Berk
>>
>> ________________________________
>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michele Pellegrino <micpel at kth.se>
>> Sent: Tuesday, January 21, 2020 5:16 PM
>> To: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
>> Subject: [gmx-users] .dat file from gmx densmap does not match prescribed size
>>
>> Hello,
>>
>>
>> I am struggling a little bit with gmx densmap. I am trying to obtain a matrix with density values from the .dat file generated by the program; however the number of data in the output file does not match what I am expecting.
>>
>> I tried to prescribe both the number of bins in each direction (-n1 and -n2 options) and the grid size (-bin option), not at the same, of course:
>>
>>
>> gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -n1 4772 -n2 3531
>>
>>
>> OR (equivalently):
>>
>>
>> gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -bin 0.01
>>
>>
>> In both cases I get a dimension mismatch (I expect 16849932 values but I get 4359553).
>>
>> I am using GROMACS 2019.4?.
>>
>>
>> What am I doing wrong?
>>
>>
>> Thanks for your help.
>>
>>
>> Cheers,
>>
>> Michele
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

From micpel at kth.se  Thu Jan 23 14:03:58 2020
From: micpel at kth.se (Michele Pellegrino)
Date: Thu, 23 Jan 2020 13:03:58 -0000
Subject: [gmx-users] MD simulation stops without any error/warning message
Message-ID: <1579784586380.24826@kth.se>

Hi,


today I was running a MD simulation and it stopped without any error/warning message.

It just stopped: the md.log file reported everything till the last time step, and no information on the nature of the termination can be found in the standard output and the standard error.

I tried to restart the simulation using the last checkpoint but I got the error message:

-------------------------------------------------------
Program:     gmx mdrun, version 2019.4
Source file: src/gromacs/fileio/checkpoint.cpp (line 2435)

Fatal error:
Failed to lock: md.log. Already running simulation?

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
So, I double-checked if the simulation was still running in the background (and exponentially slowed down, for some reason) or if I accidentally stopped the process in background (without killing it, though): no trace of the process to be found.
I run gmx energy with the default ener.edr file to see if it stopped because of some unphysical values for the temperature or the total energy, but everything seems to have stayed bounded.
It is actually the second time I find myself in this situation: is there another way to what find out could have gone wrong?


Thank you.


Cheers,

Michele

From micpel at kth.se  Thu Jan 23 14:09:25 2020
From: micpel at kth.se (Michele Pellegrino)
Date: Thu, 23 Jan 2020 13:09:25 -0000
Subject: [gmx-users] .dat file from gmx densmap
 doestnottmatchtprescribedtsize
In-Reply-To: <b90830a2-8d52-89a4-42d0-2658f179139a@kth.se>
References: <1579623383417.98064@kth.se>
	<AM6PR0202MB3287F8C82774E45CC9E2C3638E0C0@AM6PR0202MB3287.eurprd02.prod.outlook.com>
	<1579709255006.86755@kth.se>
	<AM6PR0202MB3287A902E6955EEA3B99A1068E0C0@AM6PR0202MB3287.eurprd02.prod.outlook.com>
	<AM6PR10MB20056D82F0B9971F3150CA1FAE0C0@AM6PR10MB2005.EURPRD10.PROD.OUTLOOK.COM>
	<51c5242e-0721-464e-6786-f26946f1426b@xray.bmc.uu.se>
	<1579730306553.39210@kth.se> <1579773835944.5857@kth.se>,
	<b90830a2-8d52-89a4-42d0-2658f179139a@kth.se>
Message-ID: <1579784962503.47439@kth.se>

You are welcome, Christian.
I see that you reported my initial message in the issue: I have to say the initial mismatch I reported was due to the script I was using for reading the file, and not to the file format itself, while the actual value for the mismatch is reported in the answer to David van der Spoel.

Thanks.

Cheers,
Michele

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Christian Blau <blau at kth.se>
Sent: 23 January 2020 13:30
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize

Hi Michele,


Thanks for the input and suggestion!


I created a redmine issue using your observations that you can follow at
https://redmine.gromacs.org/issues/3353


Best,

Christian

On 2020-01-23 11:03, Michele Pellegrino wrote:
> Ok, I believe I have found the nature of this 'quirk' looking at the source code (as Berk suggested me to do).
> I was assuming a format, but GROMACS is producing another: the .dat file in the output contains the values PLUS the coordinates for each bin, that is the first row and the first colum are not denisty values, but coordinates; hence the output matrix is indeed (n1+1)x(n2+1), the actual values being in grid[1:n1-1,1:n2-1] (0-start index convention).
> So apparently is not a bug in the code, but just a misunderstanding of me as user; I double checked the documentation (both for 2019.04 and for the new 2020 release) and I did not find any reference to the format of the output file: could it be a good idea to incude some indication in that regard?
>
> Cheers,
> Michele
>
> * there is a typo in the original message (2:n2-2 instead of 1:n2-1)
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michele Pellegrino <micpel at kth.se>
> Sent: 22 January 2020 22:58
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize
>
> I tried just now: it did not work: 1728 values expected, 1645 values in the .dat file.
> I managed to make it work by defining the number of values in each direction as (in Python):
> Nx = np.sqrt(Nda*Lx/Lz)
> Nz = Nx*Lz/Lx
> Nx = int( np.round(Nx) )
> Nz = int( np.round(Nz) )
> being Nda the number of values in the .dat file and Lx (resp. Lz) the lenght of the simulation box in the x (z) direction (np stands for numpy).
> However, I believe this manipulation should not be necessary.
>
> Cheers,
> Michele
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of David van der Spoel <spoel at xray.bmc.uu.se>
> Sent: 22 January 2020 22:07
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize
>
> Den 2020-01-22 kl. 18:44, skrev Michele Pellegrino:
>> Ok, thank you.
>> I am counting the elements assuming they are in an array organized in a row major fashion.
> have you tried supplying -n1 47 -n2 35 to be able to check manually?
>
> (by the way a resolution of 0.1 Angstrom is unlikely to give you a
> smooth surface)
>> Scarica Outlook per Android<https://aka.ms/ghei36>
>> ________________________________
>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Berk Hess <gmx3 at hotmail.com>
>> Sent: Wednesday, January 22, 2020 6:34:47 PM
>> To: gmx-users at gromacs.org <gmx-users at gromacs.org>
>> Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed size
>>
>> A grid element
>>
>> I looked at the code and it directly uses n1 and n2 you provide. So I thought that it might be that the code reading the file has a limit on the number of characters on a line.
>>
>> /Berk
>>
>> ________________________________
>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michele Pellegrino <micpel at kth.se>
>> Sent: Wednesday, January 22, 2020 5:07 PM
>> To: gmx-users at gromacs.org <gmx-users at gromacs.org>
>> Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed size
>>
>>
>> What do you mean by 'element'?
>>
>> Anyway, part of the issue was in how I was reading the file; with a little modification of the script I reduced the mismatch, but it still persists.
>> Could it be because GROMACS forces a grid with same meshwith in x and (in my case) z direction, so that the used should impose either -n1 OR -n2 (but not both)? Or maybe the issue is just in the format of the .dat output file?
>>
>> By the way, the simulation box is 47.72970  x 5.51140 x 35.37240 nanometers (if that may help understanding the issue).
>>
>> Thanks,
>> Michele
>>
>> ________________________________________
>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Berk Hess <gmx3 at hotmail.com>
>> Sent: 22 January 2020 16:49
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] .dat file from gmx densmap does not match      prescribed      size
>>
>> How are you counting the elements? Lines with 3531 elements are very long, so they can easily exceed some limit.
>>
>> /Berk
>>
>> ________________________________
>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michele Pellegrino <micpel at kth.se>
>> Sent: Tuesday, January 21, 2020 5:16 PM
>> To: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
>> Subject: [gmx-users] .dat file from gmx densmap does not match prescribed size
>>
>> Hello,
>>
>>
>> I am struggling a little bit with gmx densmap. I am trying to obtain a matrix with density values from the .dat file generated by the program; however the number of data in the output file does not match what I am expecting.
>>
>> I tried to prescribe both the number of bins in each direction (-n1 and -n2 options) and the grid size (-bin option), not at the same, of course:
>>
>>
>> gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -n1 4772 -n2 3531
>>
>>
>> OR (equivalently):
>>
>>
>> gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -bin 0.01
>>
>>
>> In both cases I get a dimension mismatch (I expect 16849932 values but I get 4359553).
>>
>> I am using GROMACS 2019.4?.
>>
>>
>> What am I doing wrong?
>>
>>
>> Thanks for your help.
>>
>>
>> Cheers,
>>
>> Michele
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

From alessandra.villa.biosim at gmail.com  Thu Jan 23 14:39:02 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Thu, 23 Jan 2020 13:39:02 -0000
Subject: [gmx-users] MD simulation stops without any error/warning
	message
In-Reply-To: <1579784586380.24826@kth.se>
References: <1579784586380.24826@kth.se>
Message-ID: <CANogp5yq+4NT87z9nK0HpSxzRgnb+7ky6j7z-UfKnTu0eENwrQ@mail.gmail.com>

Hi,

On Thu, Jan 23, 2020 at 2:04 PM Michele Pellegrino <micpel at kth.se> wrote:

> Hi,
>
>
> today I was running a MD simulation and it stopped without any
> error/warning message.
>
> It just stopped: the md.log file reported everything till the last time
> step, and no information on the nature of the termination can be found in
> the standard output and the standard error.
>
> I tried to restart the simulation using the last checkpoint but I got the
> error message:
>
> -------------------------------------------------------
> Program:     gmx mdrun, version 2019.4
> Source file: src/gromacs/fileio/checkpoint.cpp (line 2435)
>
> Fatal error:
> Failed to lock: md.log. Already running simulation?
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> So, I double-checked if the simulation was still running in the background
> (and exponentially slowed down, for some reason) or if I accidentally
> stopped the process in background (without killing it, though): no trace of
> the process to be found.
> I run gmx energy with the default ener.edr file to see if it stopped
> because of some unphysical values for the temperature or the total energy,
> but everything seems to have stayed bounded.
> It is actually the second time I find myself in this situation: is there
> another way to what find out could have gone wrong?
>
>
If  a core file was generated , you could look at it

Best regards
Alessandra

>
> Thank you.
>
>
> Cheers,
>
> Michele
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Thu Jan 23 14:39:05 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Thu, 23 Jan 2020 13:39:05 -0000
Subject: [gmx-users] MD simulation stops without any error/warning
	message
In-Reply-To: <1579784586380.24826@kth.se>
References: <1579784586380.24826@kth.se>
Message-ID: <CANogp5yq+4NT87z9nK0HpSxzRgnb+7ky6j7z-UfKnTu0eENwrQ@mail.gmail.com>

Hi,

On Thu, Jan 23, 2020 at 2:04 PM Michele Pellegrino <micpel at kth.se> wrote:

> Hi,
>
>
> today I was running a MD simulation and it stopped without any
> error/warning message.
>
> It just stopped: the md.log file reported everything till the last time
> step, and no information on the nature of the termination can be found in
> the standard output and the standard error.
>
> I tried to restart the simulation using the last checkpoint but I got the
> error message:
>
> -------------------------------------------------------
> Program:     gmx mdrun, version 2019.4
> Source file: src/gromacs/fileio/checkpoint.cpp (line 2435)
>
> Fatal error:
> Failed to lock: md.log. Already running simulation?
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> So, I double-checked if the simulation was still running in the background
> (and exponentially slowed down, for some reason) or if I accidentally
> stopped the process in background (without killing it, though): no trace of
> the process to be found.
> I run gmx energy with the default ener.edr file to see if it stopped
> because of some unphysical values for the temperature or the total energy,
> but everything seems to have stayed bounded.
> It is actually the second time I find myself in this situation: is there
> another way to what find out could have gone wrong?
>
>
If  a core file was generated , you could look at it

Best regards
Alessandra

>
> Thank you.
>
>
> Cheers,
>
> Michele
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From micpel at kth.se  Thu Jan 23 15:35:50 2020
From: micpel at kth.se (Michele Pellegrino)
Date: Thu, 23 Jan 2020 14:35:50 -0000
Subject: [gmx-users] MD simulation stops without any
	error/warning	message
In-Reply-To: <CANogp5yq+4NT87z9nK0HpSxzRgnb+7ky6j7z-UfKnTu0eENwrQ@mail.gmail.com>
References: <1579784586380.24826@kth.se>,
	<CANogp5yq+4NT87z9nK0HpSxzRgnb+7ky6j7z-UfKnTu0eENwrQ@mail.gmail.com>
Message-ID: <1579790113278.10584@kth.se>

Alessandra, no core file was generated: I 'only' have the trajectory, the checkpoint state, the .edr file and the md.log file; none of them report an error message whatsoever.
The only thing that comes to my mind is a crash because of a failure of the SIMD (I have set AVX2_128 when building GROMACS), could it be?
Thank you for the suggestion by the way.

Cheers,
Michele
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Alessandra Villa <alessandra.villa.biosim at gmail.com>
Sent: 23 January 2020 14:38
To: gmx-users at gromacs.org; gromacs.org_gmx-users
Subject: Re: [gmx-users] MD simulation stops without any error/warning  message

Hi,

On Thu, Jan 23, 2020 at 2:04 PM Michele Pellegrino <micpel at kth.se> wrote:

> Hi,
>
>
> today I was running a MD simulation and it stopped without any
> error/warning message.
>
> It just stopped: the md.log file reported everything till the last time
> step, and no information on the nature of the termination can be found in
> the standard output and the standard error.
>
> I tried to restart the simulation using the last checkpoint but I got the
> error message:
>
> -------------------------------------------------------
> Program:     gmx mdrun, version 2019.4
> Source file: src/gromacs/fileio/checkpoint.cpp (line 2435)
>
> Fatal error:
> Failed to lock: md.log. Already running simulation?
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> So, I double-checked if the simulation was still running in the background
> (and exponentially slowed down, for some reason) or if I accidentally
> stopped the process in background (without killing it, though): no trace of
> the process to be found.
> I run gmx energy with the default ener.edr file to see if it stopped
> because of some unphysical values for the temperature or the total energy,
> but everything seems to have stayed bounded.
> It is actually the second time I find myself in this situation: is there
> another way to what find out could have gone wrong?
>
>
If  a core file was generated , you could look at it

Best regards
Alessandra

>
> Thank you.
>
>
> Cheers,
>
> Michele
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

From nikolaev at spbau.ru  Thu Jan 23 15:52:32 2020
From: nikolaev at spbau.ru (nikolaev at spbau.ru)
Date: Thu, 23 Jan 2020 14:52:32 -0000
Subject: [gmx-users] Calculation of an energy term for stretching
Message-ID: <0c49b8fe40fc48ad111b9db56216b3b1.squirrel@mail.spbau.ru>

Dear collegues,

I am trying to write an energy function for my molecule that will imitate
the results of the amber energy function. For this reason, I calculated
all energy terms for my molecule (printed all terms for the 0-th step in
energy minimization).
However, I find a problem in the very first formula: a harmonic potential
for bond stretching. I get the results twice as large as gromacs.
I use amber potential. The force constants are of magnitude ~250 000.0
I apply the formula k/2 (b - b0)^2. Amber99 force field.
Where can the problem come from?

My molecular system is a molecule of 57 atoms, in vacuum.

Best,
Dmitrii





From travis.meyer at rutgers.edu  Thu Jan 23 19:33:39 2020
From: travis.meyer at rutgers.edu (Travis Meyer)
Date: Thu, 23 Jan 2020 18:33:39 -0000
Subject: [gmx-users] gmx distance error - invalid index with -f vs -s input
	file
Message-ID: <BN8PR14MB3171FE4A28ED888D64591776930F0@BN8PR14MB3171.namprd14.prod.outlook.com>

Hello all,

I am using gmx distance to extract bond distances from a set of 200 coarse-grained polymer molecules (10 "atoms" each). I created an index file pointing to all of the bonds, and ran the command as

gmx distance -f cg_traj.gro -n bonds.ndx -oh bondhist.xvg

However, I was getting an error message upon choosing which index group to use.

"Inconsistency in user input: Invalid index group references encountered Group 'bonds'cannot be used in selections, because it contains negative atom indices and/or references atoms not present (largest allowed atom index is 0)."

Both the .gro and .ndx file contain the correct atom indices (1-2000). Interestingly enough, when I sent the same .gro file to gmx distance using the -s tag, I was able to correctly get the bond distance histogram (albeit I do not believe it includes all time points from the trajectory).

Does anyone have any insight onto why switching from an input trajectory (-f) to an input structure (-s) using the same .gro file would alleviate the error above, or what could be causing that error when sending a trajectory? I am new to GROMACS/Molecular Dynamics, so any help would be greatly appreciated.

Thanks,
Travis Meyer, Ph.D.
INSPIRE Postdoctoral Fellow
Gormley Lab, Rutgers University

From yogesh.rma13 at gmail.com  Fri Jan 24 08:16:03 2020
From: yogesh.rma13 at gmail.com (Yogesh Sharma)
Date: Fri, 24 Jan 2020 07:16:03 -0000
Subject: [gmx-users] Protein pore collapse during simulation.
Message-ID: <CACWq+68ZcG2JNbK_vXEt4bCa4pmLoCSj=-5wS9BWa8vuCWphFw@mail.gmail.com>

Sir,
 If i want to use charmm gui generated assembly for simulation in gromac
forcefield. How can i extract berger lipid parameters (i.e lipid.itp
according to yout tutorial) corresponding to charmm nomenclature? so that i
can modify my forcefield in accordance.

my ultimate aim is to simulate membrane protein with a ligand. whose
parameters are only available in gromacff (ATB). #ligand contain metalloid
atoms.

*with  regards*
*Yogesh Sharma*

From alessandra.villa.biosim at gmail.com  Fri Jan 24 08:57:41 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Fri, 24 Jan 2020 07:57:41 -0000
Subject: [gmx-users] Calculation of an energy term for stretching
In-Reply-To: <0c49b8fe40fc48ad111b9db56216b3b1.squirrel@mail.spbau.ru>
References: <0c49b8fe40fc48ad111b9db56216b3b1.squirrel@mail.spbau.ru>
Message-ID: <CANogp5zoWHBGR9nQQUjUHmrZk7ZTZfBFV2XpUfz++L4M12UmMQ@mail.gmail.com>

Hi,

Below some suggestions
On Thu, Jan 23, 2020 at 3:52 PM <nikolaev at spbau.ru> wrote:

> Dear collegues,
>
> I am trying to write an energy function for my molecule that will imitate
> the results of the amber energy function. For this reason, I calculated
> all energy terms for my molecule (printed all terms for the 0-th step in
> energy minimization).
> However, I find a problem in the very first formula: a harmonic potential
> for bond stretching. I get the results twice as large as gromacs.
> I use amber potential. The force constants are of magnitude ~250 000.0
> I apply the formula k/2 (b - b0)^2. Amber99 force field.
> Where can the problem come from?
>
>
Maybe a bad unit conversion while you convert the dimension to GROMACS unit
(see
http://manual.gromacs.org/documentation/2019-current/reference-manual/definitions.html?highlight=gromacs%20unit
)
Maybe a difference in the analytical formula in GROMACS for the
potentialthe one use in AMBER  ( e.i k vs k/2 )
For interaction potential formula see
http://manual.gromacs.org/documentation/2019-current/reference-manual/functions.html
For the potential format see Table 14 in

http://manual.gromacs.org/documentation/2019-current/reference-manual/topologies/topology-file-formats.html?highlight=table%20force%20field
Best regards
Alessandra



> My molecular system is a molecule of 57 atoms, in vacuum.
>
> Best,
> Dmitrii
>
>
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Fri Jan 24 08:57:42 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Fri, 24 Jan 2020 07:57:42 -0000
Subject: [gmx-users] Calculation of an energy term for stretching
In-Reply-To: <0c49b8fe40fc48ad111b9db56216b3b1.squirrel@mail.spbau.ru>
References: <0c49b8fe40fc48ad111b9db56216b3b1.squirrel@mail.spbau.ru>
Message-ID: <CANogp5zoWHBGR9nQQUjUHmrZk7ZTZfBFV2XpUfz++L4M12UmMQ@mail.gmail.com>

Hi,

Below some suggestions
On Thu, Jan 23, 2020 at 3:52 PM <nikolaev at spbau.ru> wrote:

> Dear collegues,
>
> I am trying to write an energy function for my molecule that will imitate
> the results of the amber energy function. For this reason, I calculated
> all energy terms for my molecule (printed all terms for the 0-th step in
> energy minimization).
> However, I find a problem in the very first formula: a harmonic potential
> for bond stretching. I get the results twice as large as gromacs.
> I use amber potential. The force constants are of magnitude ~250 000.0
> I apply the formula k/2 (b - b0)^2. Amber99 force field.
> Where can the problem come from?
>
>
Maybe a bad unit conversion while you convert the dimension to GROMACS unit
(see
http://manual.gromacs.org/documentation/2019-current/reference-manual/definitions.html?highlight=gromacs%20unit
)
Maybe a difference in the analytical formula in GROMACS for the
potentialthe one use in AMBER  ( e.i k vs k/2 )
For interaction potential formula see
http://manual.gromacs.org/documentation/2019-current/reference-manual/functions.html
For the potential format see Table 14 in

http://manual.gromacs.org/documentation/2019-current/reference-manual/topologies/topology-file-formats.html?highlight=table%20force%20field
Best regards
Alessandra



> My molecular system is a molecule of 57 atoms, in vacuum.
>
> Best,
> Dmitrii
>
>
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Fri Jan 24 09:33:30 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Fri, 24 Jan 2020 08:33:30 -0000
Subject: [gmx-users] gmx distance error - invalid index with -f vs -s
 input file
In-Reply-To: <BN8PR14MB3171FE4A28ED888D64591776930F0@BN8PR14MB3171.namprd14.prod.outlook.com>
References: <BN8PR14MB3171FE4A28ED888D64591776930F0@BN8PR14MB3171.namprd14.prod.outlook.com>
Message-ID: <CANogp5zF3Kh_NT4bddG7gwLCHy61kU7cNX0xb+NV5mhW_q9=gg@mail.gmail.com>

Hi,
see below

On Thu, Jan 23, 2020 at 7:34 PM Travis Meyer <travis.meyer at rutgers.edu>
wrote:

> Hello all,
>
> I am using gmx distance to extract bond distances from a set of 200
> coarse-grained polymer molecules (10 "atoms" each). I created an index file
> pointing to all of the bonds, and ran the command as
>
> gmx distance -f cg_traj.gro -n bonds.ndx -oh bondhist.xvg
>
> However, I was getting an error message upon choosing which index group to
> use.
>
> "Inconsistency in user input: Invalid index group references encountered
> Group 'bonds'cannot be used in selections, because it contains negative
> atom indices and/or references atoms not present (largest allowed atom
> index is 0)."
>
>
it looks that there is something wrong in reading your cg_traj.gro file
(probably similar to what you had before with xtc file). Did you try to
visualize  cg_traj.gro using VMD (for example).



> Both the .gro and .ndx file contain the correct atom indices (1-2000).
> Interestingly enough, when I sent the same .gro file to gmx distance using
> the -s tag, I was able to correctly get the bond distance histogram (albeit
> I do not believe it includes all time points from the trajectory).
>
> gro/xtc file contains mainly  information on the coordinates of the
particles in the system. All other information related the particles
(types/connectivity/interaction parameters and so on) are in  .tpr file.
But this file contains also the starting structure of your simulation. Thus
I suggest to check again structural file (gro and xtc) - As far as I
understood  gmx distance -f cg_traj.xtc -s *.tpr -n bonds.ndx -oh
bondhist.xvg is not working.

gmx dump could also help (
http://manual.gromacs.org/documentation/2019-current/onlinehelp/gmx-dump.html?highlight=dump)
it prints the information in tpr (and also xtc file) to a standard output
in a readable format.

Best regards
Alessandra



> Does anyone have any insight onto why switching from an input trajectory
> (-f) to an input structure (-s) using the same .gro file would alleviate
> the error above, or what could be causing that error when sending a
> trajectory? I am new to GROMACS/Molecular Dynamics, so any help would be
> greatly appreciated.
>
> Thanks,
> Travis Meyer, Ph.D.
> INSPIRE Postdoctoral Fellow
> Gormley Lab, Rutgers University
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Fri Jan 24 09:33:30 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Fri, 24 Jan 2020 08:33:30 -0000
Subject: [gmx-users] gmx distance error - invalid index with -f vs -s
 input file
In-Reply-To: <BN8PR14MB3171FE4A28ED888D64591776930F0@BN8PR14MB3171.namprd14.prod.outlook.com>
References: <BN8PR14MB3171FE4A28ED888D64591776930F0@BN8PR14MB3171.namprd14.prod.outlook.com>
Message-ID: <CANogp5zF3Kh_NT4bddG7gwLCHy61kU7cNX0xb+NV5mhW_q9=gg@mail.gmail.com>

Hi,
see below

On Thu, Jan 23, 2020 at 7:34 PM Travis Meyer <travis.meyer at rutgers.edu>
wrote:

> Hello all,
>
> I am using gmx distance to extract bond distances from a set of 200
> coarse-grained polymer molecules (10 "atoms" each). I created an index file
> pointing to all of the bonds, and ran the command as
>
> gmx distance -f cg_traj.gro -n bonds.ndx -oh bondhist.xvg
>
> However, I was getting an error message upon choosing which index group to
> use.
>
> "Inconsistency in user input: Invalid index group references encountered
> Group 'bonds'cannot be used in selections, because it contains negative
> atom indices and/or references atoms not present (largest allowed atom
> index is 0)."
>
>
it looks that there is something wrong in reading your cg_traj.gro file
(probably similar to what you had before with xtc file). Did you try to
visualize  cg_traj.gro using VMD (for example).



> Both the .gro and .ndx file contain the correct atom indices (1-2000).
> Interestingly enough, when I sent the same .gro file to gmx distance using
> the -s tag, I was able to correctly get the bond distance histogram (albeit
> I do not believe it includes all time points from the trajectory).
>
> gro/xtc file contains mainly  information on the coordinates of the
particles in the system. All other information related the particles
(types/connectivity/interaction parameters and so on) are in  .tpr file.
But this file contains also the starting structure of your simulation. Thus
I suggest to check again structural file (gro and xtc) - As far as I
understood  gmx distance -f cg_traj.xtc -s *.tpr -n bonds.ndx -oh
bondhist.xvg is not working.

gmx dump could also help (
http://manual.gromacs.org/documentation/2019-current/onlinehelp/gmx-dump.html?highlight=dump)
it prints the information in tpr (and also xtc file) to a standard output
in a readable format.

Best regards
Alessandra



> Does anyone have any insight onto why switching from an input trajectory
> (-f) to an input structure (-s) using the same .gro file would alleviate
> the error above, or what could be causing that error when sending a
> trajectory? I am new to GROMACS/Molecular Dynamics, so any help would be
> greatly appreciated.
>
> Thanks,
> Travis Meyer, Ph.D.
> INSPIRE Postdoctoral Fellow
> Gormley Lab, Rutgers University
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From lalehan.ozalp at gmail.com  Fri Jan 24 12:36:19 2020
From: lalehan.ozalp at gmail.com (Lalehan Ozalp)
Date: Fri, 24 Jan 2020 11:36:19 -0000
Subject: [gmx-users] cannot load the xtc file (without PBC) to VMD
In-Reply-To: <20200114172730.Horde.XOFN7xBMtbeJ6JWeagMqDAk@mailweb.iacs.res.in>
References: <CAKpt5Pe_zAOZiK18s3V_tzGiHZ3mFkK2e7dfD=7SsocgWYk6rw@mail.gmail.com>
	<20200113201632.Horde.ujWF-BePEwYbkgA1VPqH-k7@mailweb.iacs.res.in>
	<CAKpt5Pfma8i1+Q2D1Fye7sC8QeQfv+5QiDZUfS458_+XuKf2nA@mail.gmail.com>
	<20200114172730.Horde.XOFN7xBMtbeJ6JWeagMqDAk@mailweb.iacs.res.in>
Message-ID: <CAKpt5PcWEJfcQ6wkjXOkttojMpx9HQ_XS94c4i=qYaz1tv_pcA@mail.gmail.com>

Hey again, sorry for the late reply. I meant, I didn't have the chance to
do that since a .trr file after the simulation was not generated. All I had
was the em.trr. Later, I solved the problem by using editconf. Thank you
for your attention.

On Tue, Jan 14, 2020 at 2:51 PM <spss4 at iacs.res.in> wrote:

>   I didn't get you. So your problem is solved using trr file or not?
> ----- Message from Lalehan Ozalp <lalehan.ozalp at gmail.com> ---------
>     Date: Tue, 14 Jan 2020 12:53:54 +0300
>     From: Lalehan Ozalp <lalehan.ozalp at gmail.com>
> Reply-To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] cannot load the xtc file (without PBC) to VMD
>       To: gmx-users at gromacs.org
>
> > Thank you, but I haven't tried with a trr file and actually the last .trr
> > file I've produced is em.trr.
> > Thanks,
> >
> > On Mon, Jan 13, 2020 at 5:40 PM <spss4 at iacs.res.in> wrote:
> >
> >> Hii
> >> Have you tried with the .trr file? Try the same procedure with .trr
> file.
> >> Thanks
> >> ----- Message from Lalehan Ozalp <lalehan.ozalp at gmail.com> ---------
> >>     Date: Mon, 13 Jan 2020 13:35:01 +0300
> >>     From: Lalehan Ozalp <lalehan.ozalp at gmail.com>
> >> Reply-To: gmx-users at gromacs.org
> >> Subject: [gmx-users] cannot load the xtc file (without PBC) to VMD
> >>       To: gmx-users at gromacs.org
> >>
> >> Dear all, I have a question regarding loading .xtc file (with no
> periodic
> >> boundary conditions) to VMD which I generated before. To this end, I had
> >> used the command:
> >> trjconv -f md_0_10.xtc -s md_30.tpr -n index.ndx -o noPBC.xtc -pbc mol
> >> -ur
> >> compact -center
> >> and selected *protein* for centering, and *system* for output.
> >> However, when I load my corresponding gro file to VMD, and then loading
> >> the
> >> xtc file above, the following error occurs:
> >>
> >> ERROR) BaseMolecule: attempt to init atoms while structure building in
> >> progress!
> >> ERROR) Invalid number of atoms in file: 132259
> >> Info) Using plugin xtc for coordinates from file
> >> /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc
> >> ERROR) Incorrect number of atoms (132259) in
> >> ERROR) coordinate file
> >> /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc
> >> ERROR) Mismatch between existing molecule or structure file atom count
> >> and
> >> coordinate or trajectory file atom count.
> >> Info) Finished with coordinate file
> >> /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc.
> >>
> >> This is especially strange since I carried out the same procedure
> several
> >> times before. Additionally, I have a parallel system (with an isoenzyme
> >> of
> >> the enzyme used here, with the same cofactor and the same ligand) and
> the
> >> same steps worked perfectly. As a side note, this happens when I load
> xtc
> >> file without PBC, while does not happen when I load xtc file in the
> >> presence of PBC.
> >>
> >> Thank you so much in advance!
> >> Lalehan
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests
> >> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> >> or
> >> send a mail to gmx-users-request at gromacs.org.
> >>
> >> ----- End message from Lalehan Ozalp <lalehan.ozalp at gmail.com> -----
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests
> > visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > send a mail to gmx-users-request at gromacs.org.
>
> ----- End message from Lalehan Ozalp <lalehan.ozalp at gmail.com> -----
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

From sadafrani6 at gmail.com  Fri Jan 24 13:22:23 2020
From: sadafrani6 at gmail.com (Sadaf Rani)
Date: Fri, 24 Jan 2020 12:22:23 -0000
Subject: [gmx-users] (no subject)
Message-ID: <CAH9Uu9O_JF3=M10ssOM1BnCxTvKb4kBJEjusshuVknHwxgCGUg@mail.gmail.com>

Dear Gromacs users
I am running a free energy calculation of the protein-ligand complex.
During the energy minimization process, I am getting many jumps in steps as
below:-

Step           Time
          10500    10500.00000

   Energies (kJ/mol)
           Bond Restraint Pot.          Angle    Proper Dih.  Improper Dih.
    1.20860e+03    1.65864e+00    4.67218e+03    1.83350e+04    1.87873e+02
          LJ-14     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)
    6.81295e+03    7.12692e+04    3.37954e+05   -6.56537e+03   -2.70668e+06
   Coul. recip.    Angle Rest.     Dih. Rest.      Potential Pres. DC (bar)
    4.78029e+03    5.32468e+00    3.32764e+00   -2.26802e+06    0.00000e+00
 Pressure (bar)    dVremain/dl       dEkin/dl      dVcoul/dl       dVvdw/dl
   -2.69428e+04    0.00000e+00    0.00000e+00    2.78529e+03   -1.65404e+02
 dVrestraint/dl   Constr. rmsd
    0.00000e+00    2.71623e-06

           Step           Time
          10501    10501.00000

           Step           Time
          10502    10502.00000

           Step           Time
          10503    10503.00000

           Step           Time
          10504    10504.00000

           Step           Time
          10505    10505.00000

           Step           Time
          10506    10506.00000

           Step           Time
          10507    10507.00000

           Step           Time
          10508    10508.00000

           Step           Time
          10509    10509.00000

           Step           Time
          10510    10510.00000

           Step           Time
          10511    10511.00000


Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 10 (which may not be possible for your system).
It
stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

Steepest Descents converged to machine precision in 10512 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -2.2680185e+06
Maximum force     =  6.3521606e+02 on atom 4653
Norm of force     =  3.6713926e+00

Should I use double precision for energy minimization?
I need your suggestions,
 please.

Thanks

Sadaf Rani

From sadafrani6 at gmail.com  Fri Jan 24 13:23:38 2020
From: sadafrani6 at gmail.com (Sadaf Rani)
Date: Fri, 24 Jan 2020 12:23:38 -0000
Subject: [gmx-users] Fwd:
In-Reply-To: <CAH9Uu9O_JF3=M10ssOM1BnCxTvKb4kBJEjusshuVknHwxgCGUg@mail.gmail.com>
References: <CAH9Uu9O_JF3=M10ssOM1BnCxTvKb4kBJEjusshuVknHwxgCGUg@mail.gmail.com>
Message-ID: <CAH9Uu9Oi4Tq6NbWsQ2VbWpR_DYgfQk29XbX08Si58Cyc6kiXYQ@mail.gmail.com>

Energy minimization getting jumps

Dear Gromacs users
I am running a free energy calculation of the protein-ligand complex.
During the energy minimization process, I am getting many jumps in steps as
below:-

Step           Time
          10500    10500.00000

   Energies (kJ/mol)
           Bond Restraint Pot.          Angle    Proper Dih.  Improper Dih.
    1.20860e+03    1.65864e+00    4.67218e+03    1.83350e+04    1.87873e+02
          LJ-14     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)
    6.81295e+03    7.12692e+04    3.37954e+05   -6.56537e+03   -2.70668e+06
   Coul. recip.    Angle Rest.     Dih. Rest.      Potential Pres. DC (bar)
    4.78029e+03    5.32468e+00    3.32764e+00   -2.26802e+06    0.00000e+00
 Pressure (bar)    dVremain/dl       dEkin/dl      dVcoul/dl       dVvdw/dl
   -2.69428e+04    0.00000e+00    0.00000e+00    2.78529e+03   -1.65404e+02
 dVrestraint/dl   Constr. rmsd
    0.00000e+00    2.71623e-06

           Step           Time
          10501    10501.00000

           Step           Time
          10502    10502.00000

           Step           Time
          10503    10503.00000

           Step           Time
          10504    10504.00000

           Step           Time
          10505    10505.00000

           Step           Time
          10506    10506.00000

           Step           Time
          10507    10507.00000

           Step           Time
          10508    10508.00000

           Step           Time
          10509    10509.00000

           Step           Time
          10510    10510.00000

           Step           Time
          10511    10511.00000


Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 10 (which may not be possible for your system).
It
stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

Steepest Descents converged to machine precision in 10512 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -2.2680185e+06
Maximum force     =  6.3521606e+02 on atom 4653
Norm of force     =  3.6713926e+00

Should I use double precision for energy minimization?
I need your suggestions,
 please.

Thanks

Sadaf Rani

From vuqv.phys at gmail.com  Fri Jan 24 14:29:47 2020
From: vuqv.phys at gmail.com (Quyen V. Vu)
Date: Fri, 24 Jan 2020 13:29:47 -0000
Subject: [gmx-users] (no subject)
In-Reply-To: <CAH9Uu9O_JF3=M10ssOM1BnCxTvKb4kBJEjusshuVknHwxgCGUg@mail.gmail.com>
References: <CAH9Uu9O_JF3=M10ssOM1BnCxTvKb4kBJEjusshuVknHwxgCGUg@mail.gmail.com>
Message-ID: <CA+CKAfzPKNqR1F=EW0zenM-hC5X6WT93+cCSLzBQ-kERjZGs4g@mail.gmail.com>

for what reasons you request the largest force in your system smaller than
such small value?

On Fri, Jan 24, 2020 at 1:22 PM Sadaf Rani <sadafrani6 at gmail.com> wrote:

> Dear Gromacs users
> I am running a free energy calculation of the protein-ligand complex.
> During the energy minimization process, I am getting many jumps in steps as
> below:-
>
> Step           Time
>           10500    10500.00000
>
>    Energies (kJ/mol)
>            Bond Restraint Pot.          Angle    Proper Dih.  Improper Dih.
>     1.20860e+03    1.65864e+00    4.67218e+03    1.83350e+04    1.87873e+02
>           LJ-14     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)
>     6.81295e+03    7.12692e+04    3.37954e+05   -6.56537e+03   -2.70668e+06
>    Coul. recip.    Angle Rest.     Dih. Rest.      Potential Pres. DC (bar)
>     4.78029e+03    5.32468e+00    3.32764e+00   -2.26802e+06    0.00000e+00
>  Pressure (bar)    dVremain/dl       dEkin/dl      dVcoul/dl       dVvdw/dl
>    -2.69428e+04    0.00000e+00    0.00000e+00    2.78529e+03   -1.65404e+02
>  dVrestraint/dl   Constr. rmsd
>     0.00000e+00    2.71623e-06
>
>            Step           Time
>           10501    10501.00000
>
>            Step           Time
>           10502    10502.00000
>
>            Step           Time
>           10503    10503.00000
>
>            Step           Time
>           10504    10504.00000
>
>            Step           Time
>           10505    10505.00000
>
>            Step           Time
>           10506    10506.00000
>
>            Step           Time
>           10507    10507.00000
>
>            Step           Time
>           10508    10508.00000
>
>            Step           Time
>           10509    10509.00000
>
>            Step           Time
>           10510    10510.00000
>
>            Step           Time
>           10511    10511.00000
>
>
> Energy minimization has stopped, but the forces have not converged to the
> requested precision Fmax < 10 (which may not be possible for your system).
> It
> stopped because the algorithm tried to make a new step whose size was too
> small, or there was no change in the energy since last step. Either way, we
> regard the minimization as converged to within the available machine
> precision, given your starting configuration and EM parameters.
>
> Double precision normally gives you higher accuracy, but this is often not
> needed for preparing to run molecular dynamics.
> You might need to increase your constraint accuracy, or turn
> off constraints altogether (set constraints = none in mdp file)
>
> Steepest Descents converged to machine precision in 10512 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  = -2.2680185e+06
> Maximum force     =  6.3521606e+02 on atom 4653
> Norm of force     =  3.6713926e+00
>
> Should I use double precision for energy minimization?
> I need your suggestions,
>  please.
>
> Thanks
>
> Sadaf Rani
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From vuqv.phys at gmail.com  Fri Jan 24 14:29:47 2020
From: vuqv.phys at gmail.com (Quyen V. Vu)
Date: Fri, 24 Jan 2020 13:29:47 -0000
Subject: [gmx-users] (no subject)
In-Reply-To: <CAH9Uu9O_JF3=M10ssOM1BnCxTvKb4kBJEjusshuVknHwxgCGUg@mail.gmail.com>
References: <CAH9Uu9O_JF3=M10ssOM1BnCxTvKb4kBJEjusshuVknHwxgCGUg@mail.gmail.com>
Message-ID: <CA+CKAfzPKNqR1F=EW0zenM-hC5X6WT93+cCSLzBQ-kERjZGs4g@mail.gmail.com>

for what reasons you request the largest force in your system smaller than
such small value?

On Fri, Jan 24, 2020 at 1:22 PM Sadaf Rani <sadafrani6 at gmail.com> wrote:

> Dear Gromacs users
> I am running a free energy calculation of the protein-ligand complex.
> During the energy minimization process, I am getting many jumps in steps as
> below:-
>
> Step           Time
>           10500    10500.00000
>
>    Energies (kJ/mol)
>            Bond Restraint Pot.          Angle    Proper Dih.  Improper Dih.
>     1.20860e+03    1.65864e+00    4.67218e+03    1.83350e+04    1.87873e+02
>           LJ-14     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)
>     6.81295e+03    7.12692e+04    3.37954e+05   -6.56537e+03   -2.70668e+06
>    Coul. recip.    Angle Rest.     Dih. Rest.      Potential Pres. DC (bar)
>     4.78029e+03    5.32468e+00    3.32764e+00   -2.26802e+06    0.00000e+00
>  Pressure (bar)    dVremain/dl       dEkin/dl      dVcoul/dl       dVvdw/dl
>    -2.69428e+04    0.00000e+00    0.00000e+00    2.78529e+03   -1.65404e+02
>  dVrestraint/dl   Constr. rmsd
>     0.00000e+00    2.71623e-06
>
>            Step           Time
>           10501    10501.00000
>
>            Step           Time
>           10502    10502.00000
>
>            Step           Time
>           10503    10503.00000
>
>            Step           Time
>           10504    10504.00000
>
>            Step           Time
>           10505    10505.00000
>
>            Step           Time
>           10506    10506.00000
>
>            Step           Time
>           10507    10507.00000
>
>            Step           Time
>           10508    10508.00000
>
>            Step           Time
>           10509    10509.00000
>
>            Step           Time
>           10510    10510.00000
>
>            Step           Time
>           10511    10511.00000
>
>
> Energy minimization has stopped, but the forces have not converged to the
> requested precision Fmax < 10 (which may not be possible for your system).
> It
> stopped because the algorithm tried to make a new step whose size was too
> small, or there was no change in the energy since last step. Either way, we
> regard the minimization as converged to within the available machine
> precision, given your starting configuration and EM parameters.
>
> Double precision normally gives you higher accuracy, but this is often not
> needed for preparing to run molecular dynamics.
> You might need to increase your constraint accuracy, or turn
> off constraints altogether (set constraints = none in mdp file)
>
> Steepest Descents converged to machine precision in 10512 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  = -2.2680185e+06
> Maximum force     =  6.3521606e+02 on atom 4653
> Norm of force     =  3.6713926e+00
>
> Should I use double precision for energy minimization?
> I need your suggestions,
>  please.
>
> Thanks
>
> Sadaf Rani
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From akash.pandya.15 at ucl.ac.uk  Fri Jan 24 21:12:26 2020
From: akash.pandya.15 at ucl.ac.uk (Pandya, Akash)
Date: Fri, 24 Jan 2020 20:12:26 -0000
Subject: [gmx-users] How to calculate the number of ligand and water
 molecules around protein?
Message-ID: <AM5PR0101MB2417361DCB2C2108FE06A25FEB0E0@AM5PR0101MB2417.eurprd01.prod.exchangelabs.com>

Hi all,

I wanted to ask about the best way to calculate the number of ligand molecules and water molecules around my protein at certain cut-off. I have used gmx trjorder -nshell  and               gmx select -os. Both have given me different results, so I wanted to know if anyone has had any luck with either to an accurate degree? Any guidance will be much appreciated.

Akash

From sli259 at g.uky.edu  Fri Jan 24 21:21:12 2020
From: sli259 at g.uky.edu (Li, Shi)
Date: Fri, 24 Jan 2020 20:21:12 -0000
Subject: [gmx-users] Build polymers with pdb2gmx
Message-ID: <CAC+hMcCuE=gwBsF+aPwY5C6dNB=uQyJLPK_a7ch4eKo2TKzpOw@mail.gmail.com>

Dear GMX users,

I am new to polymer simulation and want to build a polymer system for
Gromacs. I have followed Justin's instruction to make polyethylene by
editing the rtp and hdb file. But I have a couple of questions regarding a
larger polymer configuration:

1. The example system (polyethylene) only has one repeat unit, is there a
way to define the number of repeat unit and then generate the PDB file? I
am also wondering if there is a way to make the configuration with random
torsion? I currently use Gaussview to copy and paste, and the initial PDB
is just a linear chain. Like this...^^O^^O^^O^^
2. Since the PDB file is straightly from Gaussview, the atom names in the
file are all in basic form (C, H, O...), in order for the pdb2gmx to work,
I have to manually match and replace them according to the .rtp file. For
larger repeat unit, is there a better way to do this?

Thanks for your help and suggestions.

-- 

Shi Li

Research Assistant, Ph.D. Candidate
Department of Chemistry &
Center for Applied Energy Research (CAER)
University of Kentucky

Email: sli259 at g.uky.edu

From dburns at iastate.edu  Fri Jan 24 21:37:50 2020
From: dburns at iastate.edu (Daniel Burns)
Date: Fri, 24 Jan 2020 20:37:50 -0000
Subject: [gmx-users] T-REMD stalled - no trr files generated
Message-ID: <CAGdmtvBUD1K4=40S7i3UZmEpjCdV3TbPq-DonqH1AN0WYyrFog@mail.gmail.com>

Hi,

I have a system containing a dimer totaling about 600 residues solvated
with 32,000 water molecules.  I have 72 replicas that are spread between
300 - 406 K.  Each replica is running on 5 Intel Skylake 6140 cores.  The
simulations have been running for 14 hours and no trr files have been
generated and the md logs have not moved past the "maximum allowed distance
for charge groups involved in interactions" section.

I have run quick trials with only 4 replicas that did successfully write
trajectories and perform exchanges but the full 72 replica run never seems
to get moving.

Any thoughts?

Thank you,

Dan

From travis.meyer at rutgers.edu  Fri Jan 24 22:59:25 2020
From: travis.meyer at rutgers.edu (Travis Meyer)
Date: Fri, 24 Jan 2020 21:59:25 -0000
Subject: [gmx-users] gmx distance error - invalid index with -f vs -s input
	file
Message-ID: <BN8PR14MB317129E44B89BDF500F4BB28930E0@BN8PR14MB3171.namprd14.prod.outlook.com>

Thanks so much for your response. I have visualized the cg_traj.gro using VMD and did not observe any issues. Additionally, I was able to use cg_traj.gro to calculate bond angles using the gmx angle command along with the relevant index file without any issues. It appears to be more of a specific issue with gmx distance rather than the .gro/.xtc file itself.

One thing I am particularly intrigued by is why sending the .gro file using the -s flag works, while the -f does not?

    Thanks,
    Travis

    > Hello all,
    >
    > I am using gmx distance to extract bond distances from a set of 200
    > coarse-grained polymer molecules (10 "atoms" each). I created an index file
    > pointing to all of the bonds, and ran the command as
    >
    > gmx distance -f cg_traj.gro -n bonds.ndx -oh bondhist.xvg
    >
    > However, I was getting an error message upon choosing which index group to
    > use.
    >
    > "Inconsistency in user input: Invalid index group references encountered
    > Group 'bonds'cannot be used in selections, because it contains negative
    > atom indices and/or references atoms not present (largest allowed atom
    > index is 0)."
    >


    it looks that there is something wrong in reading your cg_traj.gro file
    (probably similar to what you had before with xtc file). Did you try to
    visualize  cg_traj.gro using VMD (for example).



    > Both the .gro and .ndx file contain the correct atom indices (1-2000).
    > Interestingly enough, when I sent the same .gro file to gmx distance using
    > the -s tag, I was able to correctly get the bond distance histogram (albeit
    > I do not believe it includes all time points from the trajectory).
    >
    > gro/xtc file contains mainly  information on the coordinates of the
    particles in the system. All other information related the particles
    (types/connectivity/interaction parameters and so on) are in  .tpr file.
    But this file contains also the starting structure of your simulation. Thus
    I suggest to check again structural file (gro and xtc) - As far as I
    understood  gmx distance -f cg_traj.xtc -s *.tpr -n bonds.ndx -oh
    bondhist.xvg is not working.

    gmx dump could also help    it prints the information in tpr (and also xtc file) to a standard output
    in a readable format.

    Best regards
    Alessandra



    > Does anyone have any insight onto why switching from an input trajectory
    > (-f) to an input structure (-s) using the same .gro file would alleviate
    > the error above, or what could be causing that error when sending a
    > trajectory? I am new to GROMACS/Molecular Dynamics, so any help would be
    > greatly appreciated.
    >
    > Thanks,
    > Travis Meyer, Ph.D.
    > INSPIRE Postdoctoral Fellow
    > Gormley Lab, Rutgers University

Travis Meyer, Ph.D.
INSPIRE Postdoctoral Fellow
Gormley Lab, Rutgers University

From sadafrani6 at gmail.com  Sat Jan 25 00:09:17 2020
From: sadafrani6 at gmail.com (Sadaf Rani)
Date: Fri, 24 Jan 2020 23:09:17 -0000
Subject: [gmx-users] list of missing interactions
Message-ID: <CAH9Uu9OuRsv1jiHq=65xB55vc_SNrrUK-JM+bcSxRUJ6KBqNCw@mail.gmail.com>

Dear Gromacs users
I am doing free energy calculation of protein-ligand complex and getting
again n again same error:-

Not all bonded interactions have been properly assigned to the domain
decomposition cells
A list of missing interactions:
          Dih. Rest. of      3 missing      1

Could anyone please suggest me how to solve this error? I have tried to
use -nt 2 -pin on in order to avoid domain decomposition.
Looking forward to hearing from you.

Thanks and regards

Sadaf

From yogesh.rma13 at gmail.com  Sat Jan 25 06:59:24 2020
From: yogesh.rma13 at gmail.com (Yogesh Sharma)
Date: Sat, 25 Jan 2020 05:59:24 -0000
Subject: [gmx-users] =?utf-8?q?choice_of_=CE=94Qm_Optimized_Energy?=
Message-ID: <CACWq+6-A1gXSggtsLza8w-PM0ZZjnwih9WaM58X2ke+JByrhQQ@mail.gmail.com>

Greetings everyone,
I was looking at the parameter files of a ligand. I found four files of
ligand  under the same name but differences were there in ?Qm Optimized
Energy
-1556371.3071 kJ.mol-1
-0.525
0.429
-0.250
which one should I use for my ligand interaction studies?
looking forward for your suggestions.

From mark.j.abraham at gmail.com  Sun Jan 26 00:17:54 2020
From: mark.j.abraham at gmail.com (Mark Abraham)
Date: Sat, 25 Jan 2020 23:17:54 -0000
Subject: [gmx-users] T-REMD stalled - no trr files generated
In-Reply-To: <CAGdmtvBUD1K4=40S7i3UZmEpjCdV3TbPq-DonqH1AN0WYyrFog@mail.gmail.com>
References: <CAGdmtvBUD1K4=40S7i3UZmEpjCdV3TbPq-DonqH1AN0WYyrFog@mail.gmail.com>
Message-ID: <CAMNuMAQGtNZX=7MYayENw6Yh9PsbOE_wEK6R9dqt40BsTiztiA@mail.gmail.com>

Hi,

Sounds like at least one replica isn't stable in its ensemble. Try a multi
run without replica exchange and see.

Mark

On Fri., 24 Jan. 2020, 21:38 Daniel Burns, <dburns at iastate.edu> wrote:

> Hi,
>
> I have a system containing a dimer totaling about 600 residues solvated
> with 32,000 water molecules.  I have 72 replicas that are spread between
> 300 - 406 K.  Each replica is running on 5 Intel Skylake 6140 cores.  The
> simulations have been running for 14 hours and no trr files have been
> generated and the md logs have not moved past the "maximum allowed distance
> for charge groups involved in interactions" section.
>
> I have run quick trials with only 4 replicas that did successfully write
> trajectories and perform exchanges but the full 72 replica run never seems
> to get moving.
>
> Any thoughts?
>
> Thank you,
>
> Dan
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From imanahmadabadi75 at gmail.com  Sun Jan 26 22:18:09 2020
From: imanahmadabadi75 at gmail.com (Iman Ahmadabadi)
Date: Sun, 26 Jan 2020 21:18:09 -0000
Subject: [gmx-users] Dipole moment and dielectric constant - gmx dipoles
Message-ID: <CAHz7aGtohbMNQEh3J_eX3O2h8GrsVGLSUYVuXbfa6RP_owSa7Q@mail.gmail.com>

Dear Gromacs users,

I'm trying to reproduce the gmx dipoles results via python code. In
calculating the fluctuations of total dipole moment, which is the sum on
dipole moment of individual molecules in the box, M = \sum q_{i}*R_{i}, in
which the charges q_{i} are in electron unit and position R_{i} are in nm.
For calculating M for each time step (frame), the x,y, and z component of
each atom is multiplied to their charges, and then summing on all atoms.
The average of M is on all trajectory frames, meaning that summing on M for
all frames and then dividing by the number of frames. Here, the acquired M
is divided by proper constant (0.020819434 e
<https://en.wikipedia.org/wiki/Elementary_charge>?nm
<https://en.wikipedia.org/wiki/Nanometre>) to set it in the Debye unit.

For M^{2}, M.M (dot product of M by M) is calculated for each frame and
then summing on all frames, followed by dividing by the number of frames.
But the results are larger than gmx dipoles, I wanted to ask that there is
something gmx dipoles is using in order to calculate the <M> and <M^2>,
causing this difference? I appreciate any help in this regard.

Best regards,
Iman

From ploche at physik.fu-berlin.de  Sun Jan 26 22:45:28 2020
From: ploche at physik.fu-berlin.de (Philip Loche)
Date: Sun, 26 Jan 2020 21:45:28 -0000
Subject: [gmx-users] Dipole moment and dielectric constant - gmx dipoles
In-Reply-To: <CAHz7aGtohbMNQEh3J_eX3O2h8GrsVGLSUYVuXbfa6RP_owSa7Q@mail.gmail.com>
References: <CAHz7aGtohbMNQEh3J_eX3O2h8GrsVGLSUYVuXbfa6RP_owSa7Q@mail.gmail.com>
Message-ID: <66069462-8250-46C4-8A33-17967814A1F0@physik.fu-berlin.de>

Dear Iman,

your approach sounds reasonable. Have you checked that all your molecules are whole? In the trajectory all atoms are located inside your simulation box. This means that some molecules are split which will lead to huge dipole moments.

Best

Philip

Sent from my phone, forgive brevity and typos

> On 26. Jan 2020, at 22:18, Iman Ahmadabadi <imanahmadabadi75 at gmail.com> wrote:
> 
> ?Dear Gromacs users,
> 
> I'm trying to reproduce the gmx dipoles results via python code. In
> calculating the fluctuations of total dipole moment, which is the sum on
> dipole moment of individual molecules in the box, M = \sum q_{i}*R_{i}, in
> which the charges q_{i} are in electron unit and position R_{i} are in nm.
> For calculating M for each time step (frame), the x,y, and z component of
> each atom is multiplied to their charges, and then summing on all atoms.
> The average of M is on all trajectory frames, meaning that summing on M for
> all frames and then dividing by the number of frames. Here, the acquired M
> is divided by proper constant (0.020819434 e
> <https://en.wikipedia.org/wiki/Elementary_charge>?nm
> <https://en.wikipedia.org/wiki/Nanometre>) to set it in the Debye unit.
> 
> For M^{2}, M.M (dot product of M by M) is calculated for each frame and
> then summing on all frames, followed by dividing by the number of frames.
> But the results are larger than gmx dipoles, I wanted to ask that there is
> something gmx dipoles is using in order to calculate the <M> and <M^2>,
> causing this difference? I appreciate any help in this regard.
> 
> Best regards,
> Iman
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.


From imanahmadabadi75 at gmail.com  Mon Jan 27 01:29:04 2020
From: imanahmadabadi75 at gmail.com (Iman Ahmadabadi)
Date: Mon, 27 Jan 2020 00:29:04 -0000
Subject: [gmx-users] Dipole moment and dielectric constant - gmx dipoles
In-Reply-To: <CAHz7aGtohbMNQEh3J_eX3O2h8GrsVGLSUYVuXbfa6RP_owSa7Q@mail.gmail.com>
References: <CAHz7aGtohbMNQEh3J_eX3O2h8GrsVGLSUYVuXbfa6RP_owSa7Q@mail.gmail.com>
Message-ID: <CAHz7aGt0bcmmbYhJNzng=rYdw6hd_zRoa-OC-1EWX8ui9onopA@mail.gmail.com>

Dear Philip,

Yes, you are right, thank you very much for your time and kindness.

Best regards,
Iman

On Sun, Jan 26, 2020 at 4:17 PM Iman Ahmadabadi <imanahmadabadi75 at gmail.com>
wrote:

> Dear Gromacs users,
>
> I'm trying to reproduce the gmx dipoles results via python code. In
> calculating the fluctuations of total dipole moment, which is the sum on
> dipole moment of individual molecules in the box, M = \sum q_{i}*R_{i}, in
> which the charges q_{i} are in electron unit and position R_{i} are in nm.
> For calculating M for each time step (frame), the x,y, and z component of
> each atom is multiplied to their charges, and then summing on all atoms.
> The average of M is on all trajectory frames, meaning that summing on M for
> all frames and then dividing by the number of frames. Here, the acquired M
> is divided by proper constant (0.020819434 e
> <https://en.wikipedia.org/wiki/Elementary_charge>?nm
> <https://en.wikipedia.org/wiki/Nanometre>) to set it in the Debye unit.
>
> For M^{2}, M.M (dot product of M by M) is calculated for each frame and
> then summing on all frames, followed by dividing by the number of frames.
> But the results are larger than gmx dipoles, I wanted to ask that there is
> something gmx dipoles is using in order to calculate the <M> and <M^2>,
> causing this difference? I appreciate any help in this regard.
>
> Best regards,
> Iman
>

From ak543714 at gmail.com  Mon Jan 27 02:43:48 2020
From: ak543714 at gmail.com (Amit Kumar)
Date: Mon, 27 Jan 2020 01:43:48 -0000
Subject: [gmx-users] Regarding REMD using gromacs 4.5.5 in the implicit
	solvent
Message-ID: <CAJSn8+Xw+niyT++-r2syA+fJ976pjjhMknyosEsV1w1zYFmz-A@mail.gmail.com>

Dear Gromacs user,
I am trying to run REMD in the implicit solvent using gromacs4.5.5 but,
unable to run the simulation. No error is found in the output file. The
only message I am getting in output file is:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/software/openmpi/lib export
PATH=/tmp/30579.1.32core.q:/home/softwares/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/libfabric/bin:/home/softwares/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin:/opt/openmpi/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/n.sengupta/.composer/vendor/bin:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/rocks/bin:/opt/rocks/sbin:/opt/gridengine/bin/lx-amd64:/home/n.sengupta/software/openmpi/bin:/home/n.sengupta/software/openmpi/bin:/home/n.sengupta/software/openmpi/bin:/home/n.sengupta/software/openmpi/bin:/home/n.sengupta/software/openmpi/bin:/home/n.sengupta/software/openmpi/bin:/home/n.sengupta/software/openmpi/bin:/home/n.sengupta/software/openmpi/bin:/home/n.sengupta/.local/bin:/home/n.sengupta/bin:/home/n.sengupta/software/openmpi/bin
Total number of replicas are 26. Can anyone help and explain what is wrong
in the script and how can I overcome this situation?

Thank You
Amit Kumar

From ak543714 at gmail.com  Mon Jan 27 02:43:48 2020
From: ak543714 at gmail.com (Amit Kumar)
Date: Mon, 27 Jan 2020 01:43:48 -0000
Subject: [gmx-users] Regarding REMD using gromacs 4.5.5 in the implicit
	solvent
Message-ID: <CAJSn8+Xw+niyT++-r2syA+fJ976pjjhMknyosEsV1w1zYFmz-A@mail.gmail.com>

Dear Gromacs user,
I am trying to run REMD in the implicit solvent using gromacs4.5.5 but,
unable to run the simulation. No error is found in the output file. The
only message I am getting in output file is:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/software/openmpi/lib export
PATH=/tmp/30579.1.32core.q:/home/softwares/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/libfabric/bin:/home/softwares/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin:/opt/openmpi/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/n.sengupta/.composer/vendor/bin:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/rocks/bin:/opt/rocks/sbin:/opt/gridengine/bin/lx-amd64:/home/n.sengupta/software/openmpi/bin:/home/n.sengupta/software/openmpi/bin:/home/n.sengupta/software/openmpi/bin:/home/n.sengupta/software/openmpi/bin:/home/n.sengupta/software/openmpi/bin:/home/n.sengupta/software/openmpi/bin:/home/n.sengupta/software/openmpi/bin:/home/n.sengupta/software/openmpi/bin:/home/n.sengupta/.local/bin:/home/n.sengupta/bin:/home/n.sengupta/software/openmpi/bin
Total number of replicas are 26. Can anyone help and explain what is wrong
in the script and how can I overcome this situation?

Thank You
Amit Kumar

From somu.chaudhari at gmail.com  Mon Jan 27 08:24:11 2020
From: somu.chaudhari at gmail.com (Somdatta Chaudhari)
Date: Mon, 27 Jan 2020 07:24:11 -0000
Subject: [gmx-users] learning gromacs
Message-ID: <CAPk+MMgtqHRBj+LKspA0E6nOmWbWc5sqiyd4zZNKJgDxJDwgrA@mail.gmail.com>

Want to learn gromacs...plz help me out in this regards

-- 
Somdatta Y. Chaudhari
M.Pharm(Pharma.Chem)
Lecturer
Dept- Pharma.Chem
Modern College of Pharmacy,
Nigdi, Pune. (India)

From spoel at xray.bmc.uu.se  Mon Jan 27 09:13:43 2020
From: spoel at xray.bmc.uu.se (David van der Spoel)
Date: Mon, 27 Jan 2020 08:13:43 -0000
Subject: [gmx-users] Dipole moment and dielectric constant - gmx dipoles
In-Reply-To: <CAHz7aGt0bcmmbYhJNzng=rYdw6hd_zRoa-OC-1EWX8ui9onopA@mail.gmail.com>
References: <CAHz7aGtohbMNQEh3J_eX3O2h8GrsVGLSUYVuXbfa6RP_owSa7Q@mail.gmail.com>
	<CAHz7aGt0bcmmbYhJNzng=rYdw6hd_zRoa-OC-1EWX8ui9onopA@mail.gmail.com>
Message-ID: <8556eed8-7ddd-53a5-2019-3aef9d107c10@xray.bmc.uu.se>

Den 2020-01-27 kl. 01:28, skrev Iman Ahmadabadi:
> Dear Philip,
> 
> Yes, you are right, thank you very much for your time and kindness.
gmx trjconv -pbc whole

> 
> Best regards,
> Iman
> 
> On Sun, Jan 26, 2020 at 4:17 PM Iman Ahmadabadi <imanahmadabadi75 at gmail.com>
> wrote:
> 
>> Dear Gromacs users,
>>
>> I'm trying to reproduce the gmx dipoles results via python code. In
>> calculating the fluctuations of total dipole moment, which is the sum on
>> dipole moment of individual molecules in the box, M = \sum q_{i}*R_{i}, in
>> which the charges q_{i} are in electron unit and position R_{i} are in nm.
>> For calculating M for each time step (frame), the x,y, and z component of
>> each atom is multiplied to their charges, and then summing on all atoms.
>> The average of M is on all trajectory frames, meaning that summing on M for
>> all frames and then dividing by the number of frames. Here, the acquired M
>> is divided by proper constant (0.020819434 e
>> <https://en.wikipedia.org/wiki/Elementary_charge>?nm
>> <https://en.wikipedia.org/wiki/Nanometre>) to set it in the Debye unit.
>>
>> For M^{2}, M.M (dot product of M by M) is calculated for each frame and
>> then summing on all frames, followed by dividing by the number of frames.
>> But the results are larger than gmx dipoles, I wanted to ask that there is
>> something gmx dipoles is using in order to calculate the <M> and <M^2>,
>> causing this difference? I appreciate any help in this regard.
>>
>> Best regards,
>> Iman
>>


-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se

From miro.astore at gmail.com  Mon Jan 27 10:25:31 2020
From: miro.astore at gmail.com (Miro Astore)
Date: Mon, 27 Jan 2020 09:25:31 -0000
Subject: [gmx-users] learning gromacs
In-Reply-To: <CAPk+MMgtqHRBj+LKspA0E6nOmWbWc5sqiyd4zZNKJgDxJDwgrA@mail.gmail.com>
References: <CAPk+MMgtqHRBj+LKspA0E6nOmWbWc5sqiyd4zZNKJgDxJDwgrA@mail.gmail.com>
Message-ID: <CAL3MGYSfUHM3KC3LT5fvetMF7-NERDv6ZKC9=kRQm7NFib-Njw@mail.gmail.com>

Hi,

I'm new to gromacs myself. Your best bet if you're new to Molecular
dynamics is to do some tutorials and read best practices to try and
understand what the computer is actually doing and why.

http://www.mdtutorials.com/gmx/
I would recommend starting with the lysozyme in water tutorial as it is the
simplest and then working through the ones that are relevant to your work.

https://www.livecomsjournal.org/article/5957-best-practices-for-foundations-in-molecular-simulations-article-v1-0
- best practice guide to help you better understand how not to waste
computer time running meaningless simulations. Just because a simulation
runs does not mean it is correct or useful.

other handy resources.
the documentation for the software.
http://manual.gromacs.org/

also googling any error messages you find will usually bring up a research
gate post or a message from this mailing list where someone has had the
same problem.

Hope this helps you getting started. Good luck.

Best, Miro

On Mon, Jan 27, 2020 at 6:24 PM Somdatta Chaudhari <somu.chaudhari at gmail.com>
wrote:

> Want to learn gromacs...plz help me out in this regards
>
> --
> Somdatta Y. Chaudhari
> M.Pharm(Pharma.Chem)
> Lecturer
> Dept- Pharma.Chem
> Modern College of Pharmacy,
> Nigdi, Pune. (India)
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From miro.astore at gmail.com  Mon Jan 27 10:25:31 2020
From: miro.astore at gmail.com (Miro Astore)
Date: Mon, 27 Jan 2020 09:25:31 -0000
Subject: [gmx-users] learning gromacs
In-Reply-To: <CAPk+MMgtqHRBj+LKspA0E6nOmWbWc5sqiyd4zZNKJgDxJDwgrA@mail.gmail.com>
References: <CAPk+MMgtqHRBj+LKspA0E6nOmWbWc5sqiyd4zZNKJgDxJDwgrA@mail.gmail.com>
Message-ID: <CAL3MGYSfUHM3KC3LT5fvetMF7-NERDv6ZKC9=kRQm7NFib-Njw@mail.gmail.com>

Hi,

I'm new to gromacs myself. Your best bet if you're new to Molecular
dynamics is to do some tutorials and read best practices to try and
understand what the computer is actually doing and why.

http://www.mdtutorials.com/gmx/
I would recommend starting with the lysozyme in water tutorial as it is the
simplest and then working through the ones that are relevant to your work.

https://www.livecomsjournal.org/article/5957-best-practices-for-foundations-in-molecular-simulations-article-v1-0
- best practice guide to help you better understand how not to waste
computer time running meaningless simulations. Just because a simulation
runs does not mean it is correct or useful.

other handy resources.
the documentation for the software.
http://manual.gromacs.org/

also googling any error messages you find will usually bring up a research
gate post or a message from this mailing list where someone has had the
same problem.

Hope this helps you getting started. Good luck.

Best, Miro

On Mon, Jan 27, 2020 at 6:24 PM Somdatta Chaudhari <somu.chaudhari at gmail.com>
wrote:

> Want to learn gromacs...plz help me out in this regards
>
> --
> Somdatta Y. Chaudhari
> M.Pharm(Pharma.Chem)
> Lecturer
> Dept- Pharma.Chem
> Modern College of Pharmacy,
> Nigdi, Pune. (India)
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From atbfiles at zoho.com  Mon Jan 27 11:37:08 2020
From: atbfiles at zoho.com (atb files)
Date: Mon, 27 Jan 2020 10:37:08 -0000
Subject: [gmx-users] Charmm to Gromacs itps
Message-ID: <16fe66a04c4.ad66ab4a133765.8415873409923566678@zoho.com>


        

        
            Hello users,I have .pdb, .psf and .crd file for one system. How to use them (convert to itp) in Gromacs??Thanks.?YogesgSent using Zoho Mail
                
            
        
        

    
    


From micpel at kth.se  Mon Jan 27 11:57:00 2020
From: micpel at kth.se (Michele Pellegrino)
Date: Mon, 27 Jan 2020 10:57:00 -0000
Subject: [gmx-users] Charmm to Gromacs itps
In-Reply-To: <16fe66a04c4.ad66ab4a133765.8415873409923566678@zoho.com>
References: <16fe66a04c4.ad66ab4a133765.8415873409923566678@zoho.com>
Message-ID: <1580122546819.67387@kth.se>

Hi,

have you tried gmx pdb2gmx -f <pdb-file-name>?

Michele
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of atb files <atbfiles at zoho.com>
Sent: 27 January 2020 10:51
To: gromacs.org_gmx-users
Subject: [gmx-users] Charmm to Gromacs itps

            Hello users,I have .pdb, .psf and .crd file for one system. How to use them (convert to itp) in Gromacs? Thanks. YogesgSent using Zoho Mail








--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

From ml.perrotta at itm.cnr.it  Mon Jan 27 12:47:28 2020
From: ml.perrotta at itm.cnr.it (Maria Luisa)
Date: Mon, 27 Jan 2020 11:47:28 -0000
Subject: [gmx-users] gmx msd
Message-ID: <38ca22f36f6f1fa06acf2dd5def10587.squirrel@webmail.itm.cnr.it>

Dear users,
I'm using the command gmx msd but I found problem when I use the option
-mol. Can u help me?

Maria Luisa


Maria Luisa Perrotta
Ph.D Student, CNR-ITM
via P.Bucci, 87036 Rende (Cs)
Italy
email: ml.perrotta at itm.cnr.it



From sinaomrani96 at gmail.com  Mon Jan 27 12:55:01 2020
From: sinaomrani96 at gmail.com (Sina Omrani)
Date: Mon, 27 Jan 2020 11:55:01 -0000
Subject: [gmx-users] Correlation Functions
Message-ID: <CADp8ML5uZHLBLvDwhR-PG_91QyAf2eCXREUdraAKiy9RYby1Ag@mail.gmail.com>

Hi,
1. Can we define a correlation function in GROMACS or we only can use those
that are already defined? If we can do it I appreciate a useful hint.
2. When I use gmx velacc command I get "Not enough trajectory frames" error
even though I used different nstvout. What frequency should I choose for
data collection? I've read the manual but there is not a rule for it.
Thank you.

From ml.perrotta at itm.cnr.it  Mon Jan 27 13:20:50 2020
From: ml.perrotta at itm.cnr.it (Maria Luisa)
Date: Mon, 27 Jan 2020 12:20:50 -0000
Subject: [gmx-users] gmx msd
Message-ID: <1adee7a6c6e28a9eeb3edf367af58e33.squirrel@webmail.itm.cnr.it>

Dear users,
I'm using the command gmx msd but I found problem when I use the option
-mol. Can u help me?

Maria Luisa


Maria Luisa Perrotta
Ph.D Student, CNR-ITM
via P.Bucci, 87036 Rende (Cs)
Italy
email: ml.perrotta at itm.cnr.it



From jalemkul at vt.edu  Mon Jan 27 15:01:17 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Mon, 27 Jan 2020 14:01:17 -0000
Subject: [gmx-users] Protein pore collapse during simulation.
In-Reply-To: <CACWq+68ZcG2JNbK_vXEt4bCa4pmLoCSj=-5wS9BWa8vuCWphFw@mail.gmail.com>
References: <CACWq+68ZcG2JNbK_vXEt4bCa4pmLoCSj=-5wS9BWa8vuCWphFw@mail.gmail.com>
Message-ID: <173960e5-7053-7eff-6929-73f4bad2a50d@vt.edu>



On 1/24/20 2:15 AM, Yogesh Sharma wrote:
> Sir,
>   If i want to use charmm gui generated assembly for simulation in gromac
> forcefield. How can i extract berger lipid parameters (i.e lipid.itp
> according to yout tutorial) corresponding to charmm nomenclature? so that i
> can modify my forcefield in accordance.

You would have to rename the atoms in the coordinate file.

> my ultimate aim is to simulate membrane protein with a ligand. whose
> parameters are only available in gromacff (ATB). #ligand contain metalloid
> atoms.

You're making a big tradeoff here, as the Berger parameters are very 
inaccurate compared to modern lipid parameter sets. Metalloids are 
generally not available in biomolecular force fields, though. At least 
look at more recent GROMOS parameter sets rather than the Berger lipids.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From jalemkul at vt.edu  Mon Jan 27 15:02:29 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Mon, 27 Jan 2020 14:02:29 -0000
Subject: [gmx-users] Build polymers with pdb2gmx
In-Reply-To: <CAC+hMcCuE=gwBsF+aPwY5C6dNB=uQyJLPK_a7ch4eKo2TKzpOw@mail.gmail.com>
References: <CAC+hMcCuE=gwBsF+aPwY5C6dNB=uQyJLPK_a7ch4eKo2TKzpOw@mail.gmail.com>
Message-ID: <1a6577ca-ad38-cde6-d8b2-35b9e010e1d6@vt.edu>



On 1/24/20 3:20 PM, Li, Shi wrote:
> Dear GMX users,
>
> I am new to polymer simulation and want to build a polymer system for
> Gromacs. I have followed Justin's instruction to make polyethylene by
> editing the rtp and hdb file. But I have a couple of questions regarding a
> larger polymer configuration:
>
> 1. The example system (polyethylene) only has one repeat unit, is there a
> way to define the number of repeat unit and then generate the PDB file? I

GROMACS has no ability to build molecules.

> am also wondering if there is a way to make the configuration with random
> torsion? I currently use Gaussview to copy and paste, and the initial PDB
> is just a linear chain. Like this...^^O^^O^^O^^

Make the linear chain and run a Langevin simulation in the gas phase.

> 2. Since the PDB file is straightly from Gaussview, the atom names in the
> file are all in basic form (C, H, O...), in order for the pdb2gmx to work,
> I have to manually match and replace them according to the .rtp file. For
> larger repeat unit, is there a better way to do this?

Unfortunately, no. Software that outputs repetitive atom names makes 
your life a nightmare when actually trying to do a simulation.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From jalemkul at vt.edu  Mon Jan 27 15:03:26 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Mon, 27 Jan 2020 14:03:26 -0000
Subject: [gmx-users] =?utf-8?q?choice_of_=CE=94Qm_Optimized_Energy?=
In-Reply-To: <CACWq+6-A1gXSggtsLza8w-PM0ZZjnwih9WaM58X2ke+JByrhQQ@mail.gmail.com>
References: <CACWq+6-A1gXSggtsLza8w-PM0ZZjnwih9WaM58X2ke+JByrhQQ@mail.gmail.com>
Message-ID: <997280b2-e54c-ca0a-f1d2-0397b3dfe4e2@vt.edu>



On 1/25/20 12:59 AM, Yogesh Sharma wrote:
> Greetings everyone,
> I was looking at the parameter files of a ligand. I found four files of
> ligand  under the same name but differences were there in ?Qm Optimized
> Energy
> -1556371.3071 kJ.mol-1
> -0.525
> 0.429
> -0.250
> which one should I use for my ligand interaction studies?

There's no way to know based on the information provided. What did you 
download? To what do those values correspond? The first number looks 
like a configurational energy in absolute QM terms but that's not a 
physical value that an MM force field can reproduce. The other values 
could correspond to any different number of properties. What are they?

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From jalemkul at vt.edu  Mon Jan 27 15:04:46 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Mon, 27 Jan 2020 14:04:46 -0000
Subject: [gmx-users] Charmm to Gromacs itps
In-Reply-To: <16fe66a04c4.ad66ab4a133765.8415873409923566678@zoho.com>
References: <16fe66a04c4.ad66ab4a133765.8415873409923566678@zoho.com>
Message-ID: <4f014a17-e2ff-e32a-2228-1e44003ab325@vt.edu>



On 1/27/20 4:51 AM, atb files wrote:
>          
>
>          
>              Hello users,I have .pdb, .psf and .crd file for one system. How to use them (convert to itp) in Gromacs??Thanks.?YogesgSent using Zoho Mail
>                  
>    

Prepare the system with CHARMM-GUI and it will give you all the 
necessary inputs for running in GROMACS.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From jalemkul at vt.edu  Mon Jan 27 15:05:24 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Mon, 27 Jan 2020 14:05:24 -0000
Subject: [gmx-users] gmx msd
In-Reply-To: <1adee7a6c6e28a9eeb3edf367af58e33.squirrel@webmail.itm.cnr.it>
References: <1adee7a6c6e28a9eeb3edf367af58e33.squirrel@webmail.itm.cnr.it>
Message-ID: <280a1f25-b0aa-88a0-c499-50992e28a71d@vt.edu>



On 1/27/20 6:20 AM, Maria Luisa wrote:
> Dear users,
> I'm using the command gmx msd but I found problem when I use the option
> -mol. Can u help me?

Not without more information. What are you doing and what is your exact 
command? What is the problem you're facing, an error? Unexpected output?

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From akash.pandya.15 at ucl.ac.uk  Mon Jan 27 15:35:00 2020
From: akash.pandya.15 at ucl.ac.uk (Pandya, Akash)
Date: Mon, 27 Jan 2020 14:35:00 -0000
Subject: [gmx-users] Diffusion Coefficient for hydration waters
Message-ID: <AM5PR0101MB2417555BB594039EF873B5A5EB0B0@AM5PR0101MB2417.eurprd01.prod.exchangelabs.com>

Hi all,

The diffusion coefficient can be calculated for the all the waters in the system, but how do calculate it for just the water molecules which are within 0.5 nm of the protein? Does anyone have any experience with this?

I've tried to use gmx select to write an index file for the waters but as this is a dynamic selection, I would have to calculate each frame individually.

Akash

From sadafrani6 at gmail.com  Mon Jan 27 16:13:32 2020
From: sadafrani6 at gmail.com (Sadaf Rani)
Date: Mon, 27 Jan 2020 15:13:32 -0000
Subject: [gmx-users] Assertion failed: Condition: bX
Message-ID: <CAH9Uu9NmFxkVtoqEHp0AkWaajDdd-jhXtZN8GFzYRV6FcR+49w@mail.gmail.com>

Dear Gromacs users

I am getting following message in my log file during MD simulation:--
-------------------------------------------------------
Program:     gmx mdrun, version 2018.1
Source file: src/gromacs/mdlib/minimize.cpp (line 582)
Function:    void write_em_traj(_IO_FILE *, t_commrec *, gmx_mdoutf *, int,
int, const char *, gmx_mtop_t *, t_inputrec *, long, em_state_t *, t_state
*, ObservablesHistory *)


*Assertion failed:Condition: bX*
The code below assumes that (with domain decomposition), x is collected to
state_global in the call above.

I could get a post regarding its fixing
https://redmine.gromacs.org/issues/2554
  Could you please suggest me why is this happening?  and how should I fix
it.

Thanks & Regards.

Sadaf

From jalemkul at vt.edu  Mon Jan 27 16:16:42 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Mon, 27 Jan 2020 15:16:42 -0000
Subject: [gmx-users] Assertion failed: Condition: bX
In-Reply-To: <CAH9Uu9NmFxkVtoqEHp0AkWaajDdd-jhXtZN8GFzYRV6FcR+49w@mail.gmail.com>
References: <CAH9Uu9NmFxkVtoqEHp0AkWaajDdd-jhXtZN8GFzYRV6FcR+49w@mail.gmail.com>
Message-ID: <b31bddf8-a6c4-5a02-8518-2530e37d807e@vt.edu>



On 1/27/20 10:13 AM, Sadaf Rani wrote:
> Dear Gromacs users
>
> I am getting following message in my log file during MD simulation:--
> -------------------------------------------------------
> Program:     gmx mdrun, version 2018.1
> Source file: src/gromacs/mdlib/minimize.cpp (line 582)
> Function:    void write_em_traj(_IO_FILE *, t_commrec *, gmx_mdoutf *, int,
> int, const char *, gmx_mtop_t *, t_inputrec *, long, em_state_t *, t_state
> *, ObservablesHistory *)
>
>
> *Assertion failed:Condition: bX*
> The code below assumes that (with domain decomposition), x is collected to
> state_global in the call above.
>
> I could get a post regarding its fixing
> https://redmine.gromacs.org/issues/2554
>    Could you please suggest me why is this happening?  and how should I fix
> it.

Upgrade to a later version of GROMACS. The Redmine issue indicates 
2018.2 has the problem, so clearly 2018.1 will, as well. At minimum, 
upgrade to the last version in the 2018 series but preferably just get 
the latest actual release.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From navneetcdl at gmail.com  Mon Jan 27 18:06:52 2020
From: navneetcdl at gmail.com (Navneet Kumar)
Date: Mon, 27 Jan 2020 17:06:52 -0000
Subject: [gmx-users] Remove water molecules from .tpr file
Message-ID: <CAOvdM4WM+=XSVPpYCS+nqDpzatg-tU4PYjUDki6hNg5rnsp4LA@mail.gmail.com>

Hello Everyone!

I want to calculate the g_mmpbsa (binding free energy) for a protein+ligand
complex.
I want to delete the water molecules and other ions from the system.
I have removed the water molecules from the .xtc file. But how to
manipulate and remove the water molecules information from .tpr
(md_0_10.tpr)file. I want a new .tpr file which matches my new trajectory
file. How to do this?

Regards
Navneet

From johnwhittake at zedat.fu-berlin.de  Mon Jan 27 18:15:30 2020
From: johnwhittake at zedat.fu-berlin.de (John Whittaker)
Date: Mon, 27 Jan 2020 17:15:30 -0000
Subject: [gmx-users] Remove water molecules from .tpr file
In-Reply-To: <CAOvdM4WM+=XSVPpYCS+nqDpzatg-tU4PYjUDki6hNg5rnsp4LA@mail.gmail.com>
References: <CAOvdM4WM+=XSVPpYCS+nqDpzatg-tU4PYjUDki6hNg5rnsp4LA@mail.gmail.com>
Message-ID: <52964.160.45.109.123.1580145328.webmail@webmail.zedat.fu-berlin.de>

Hi Navneet,

You can probably delete the water molecules and ions from your .gro file
and run all the necessary files through grompp again.

This should generate a new dummy .tpr file you can use that matches your
trajectory file.

Best,

John

> Hello Everyone!
>
> I want to calculate the g_mmpbsa (binding free energy) for a
> protein+ligand
> complex.
> I want to delete the water molecules and other ions from the system.
> I have removed the water molecules from the .xtc file. But how to
> manipulate and remove the water molecules information from .tpr
> (md_0_10.tpr)file. I want a new .tpr file which matches my new trajectory
> file. How to do this?
>
> Regards
> Navneet
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
> a mail to gmx-users-request at gromacs.org.
>



From jalemkul at vt.edu  Mon Jan 27 18:39:39 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Mon, 27 Jan 2020 17:39:39 -0000
Subject: [gmx-users] Remove water molecules from .tpr file
In-Reply-To: <52964.160.45.109.123.1580145328.webmail@webmail.zedat.fu-berlin.de>
References: <CAOvdM4WM+=XSVPpYCS+nqDpzatg-tU4PYjUDki6hNg5rnsp4LA@mail.gmail.com>
	<52964.160.45.109.123.1580145328.webmail@webmail.zedat.fu-berlin.de>
Message-ID: <df5abdad-1273-3f9b-98a6-e24fe36065bf@vt.edu>



On 1/27/20 12:15 PM, John Whittaker wrote:
> Hi Navneet,
>
> You can probably delete the water molecules and ions from your .gro file
> and run all the necessary files through grompp again.
>
> This should generate a new dummy .tpr file you can use that matches your
> trajectory file.

It's even easier than that. Just use gmx convert-tpr with a matching 
index group and it will save a new .tpr file with the desired subset of 
atoms.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From sinaomrani96 at gmail.com  Mon Jan 27 18:46:03 2020
From: sinaomrani96 at gmail.com (Sina Omrani)
Date: Mon, 27 Jan 2020 17:46:03 -0000
Subject: [gmx-users] Correlation Functions
In-Reply-To: <CADp8ML5uZHLBLvDwhR-PG_91QyAf2eCXREUdraAKiy9RYby1Ag@mail.gmail.com>
References: <CADp8ML5uZHLBLvDwhR-PG_91QyAf2eCXREUdraAKiy9RYby1Ag@mail.gmail.com>
Message-ID: <CADp8ML4pBDv8zQWY1Ny5HQbsD+BdQvdTrqk7KCxR9o-ffBfZqA@mail.gmail.com>

 Hi,
1. Can we define a correlation function in GROMACS or we only can use those
that are already defined? If we can do it I appreciate a useful hint.
2. When I use gmx velacc command I get "Not enough trajectory frames" error
even though I used different nstvout. What frequency should I choose for
data collection? I've read the manual but there is not a rule for it.
Thank you.

On Mon, 27 Jan 2020 at 15:23, Sina Omrani <sinaomrani96 at gmail.com> wrote:

> Hi,
> 1. Can we define a correlation function in GROMACS or we only can use
> those that are already defined? If we can do it I appreciate a useful hint.
> 2. When I use gmx velacc command I get "Not enough trajectory frames"
> error even though I used different nstvout. What frequency should I choose
> for data collection? I've read the manual but there is not a rule for it.
> Thank you.
>

From miro.astore at gmail.com  Tue Jan 28 02:07:49 2020
From: miro.astore at gmail.com (Miro Astore)
Date: Tue, 28 Jan 2020 01:07:49 -0000
Subject: [gmx-users] trjcat and trjconv performance
Message-ID: <CAL3MGYQkLqNmWnz8vCTFq2VL=QMygQYx91SfwE3B3jvNRSXC8w@mail.gmail.com>

Hello all.

I need to use trjcat and trjconv often and I am wondering if there is any
way to speed up these utilities. They seem quite slow at the moment
compared to the catdcd binary in the vmd distribution.

Best, Miro

From yogesh.rma13 at gmail.com  Tue Jan 28 07:38:51 2020
From: yogesh.rma13 at gmail.com (Yogesh Sharma)
Date: Tue, 28 Jan 2020 06:38:51 -0000
Subject: [gmx-users] choice of ?Qm Optimized Energy
Message-ID: <CACWq+6_sA7er1FtNOSQdW-ue9bgENahdr6MhnC6bY=5EWWbKQQ@mail.gmail.com>

thanks for your response Dr. Justin
these all values are for same ligand submitted under different molid. All
have net zero charge. only difference is in dQm optimized energy. I dont
know weather i have to choose one with lowest value or the highest. Please
check the link attached https://atb.uq.edu.au/molecule.py?molid=364968


*with  regards*
*Yogesh Sharma*

From dmaji43 at gmail.com  Tue Jan 28 08:40:40 2020
From: dmaji43 at gmail.com (Dhrubajyoti Maji)
Date: Tue, 28 Jan 2020 07:40:40 -0000
Subject: [gmx-users] TraPPE-EH in GROMACS
Message-ID: <CACrPy4Cmb2qD4Wo+XTZALDgQ_+5Y5Zg2FguDdZf7sxoEKe_4AA@mail.gmail.com>

Dear gromacs users,
        I want to use TraPPE-EH force field parameters in GROMACS-2018.3. I
have understood that in top file nbfunc=1,
comb-rule=2,fudgeLJ=0.5,fudgeQQ=0.8333. But what will be the values of
gen-pairs, nrexcl and [ pairs] section ? Any kind of help will be highly
appreciated.
Thanks and regards

Dhrubajyoti Maji

From atbfiles at zoho.com  Tue Jan 28 09:50:38 2020
From: atbfiles at zoho.com (atb files)
Date: Tue, 28 Jan 2020 08:50:38 -0000
Subject: [gmx-users] Charmm to Gromacs itps
In-Reply-To: <4f014a17-e2ff-e32a-2228-1e44003ab325@vt.edu>
References: <16fe66a04c4.ad66ab4a133765.8415873409923566678@zoho.com>
	<4f014a17-e2ff-e32a-2228-1e44003ab325@vt.edu>
Message-ID: <16feb4a73eb.c6617426182519.3166466143215009082@zoho.com>


        

        
            @Justin: the lipid is not yet added to the charmm directory. Any script?@Michele: pdb2gmx only works for proteins.-YogeshSent using Zoho Mail---- On Mon, 27 Jan 2020 19:34:34 +0530  Justin Lemkul<jalemkul at vt.edu> wrote ----On 1/27/20 4:51 AM, atb files wrote:>          >>          >              Hello users,I have .pdb, .psf and .crd file for one system. How to use them (convert to itp) in Gromacs??Thanks.?YogesgSent using Zoho Mail>                  >    Prepare the system with CHARMM-GUI and it will give you all the necessary inputs for running in GROMACS.-Justin-- ==================================================Justin A. Lemkul, Ph.D.Assistant ProfessorOffice: 301 Fralin HallLab: 303 Engel HallVirginia Tech Department of Biochemistry340 West Campus Dr.Blacksburg, VA 24061jalemkul at vt.edu | (540) 231-3129http://www.thelemkullab.com==================================================-- Gromacs Users mailing list* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists* For (un)subscribe requests visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
        
        

    
    


From inforak.007 at gmail.com  Tue Jan 28 14:53:03 2020
From: inforak.007 at gmail.com (Rakesh Bhowmick)
Date: Tue, 28 Jan 2020 13:53:03 -0000
Subject: [gmx-users] DNA-Protein complex
Message-ID: <CACD+=T9i++YFG17UrBFW2=UtvjYmEd3x5HS8ErJnvCHt8=6kXg@mail.gmail.com>

I am new in the field of molecular dynamics and simulation. I am trying to
learn online tutorial for gromacs. I have docked my DNA with protein in
HADDOCK. I want to run a simulation in gromacs. Can I make topology file of
the complex together or I need to make topology file separately. Which
forcefield should I use for DNA protein complex?

From 272699575 at qq.com  Tue Jan 28 15:09:13 2020
From: 272699575 at qq.com (=?gb18030?B?WkhBTkcgQ2hlbmc=?=)
Date: Tue, 28 Jan 2020 14:09:13 -0000
Subject: [gmx-users] Native contacts similar to "gmx mindist"
Message-ID: <tencent_BD16DECB871F5FCA6EA7973E78C6C980CC06@qq.com>

The "gmx mindist? command can output the number of contacts (numcont) between two groups as a function of time. Is there a way to only consider the native contacts, without using the PLUMED?

From micpel at kth.se  Tue Jan 28 16:46:03 2020
From: micpel at kth.se (Michele Pellegrino)
Date: Tue, 28 Jan 2020 15:46:03 -0000
Subject: [gmx-users]  COM removal note
Message-ID: <1580226360405.42830@kth.se>

Hi,


I am running some MD simulation using position restraints and turning-off centre of mass removal (comm-mode = None in the .mdp file).

However, GROMACS 2020 still tell me with a note that 'removing center of mass motion in the presence of position restraints might cause artifacts'.

So, is this note triggered by the use of restraints alone (so everything is fine), or am I doing something wrong (i.e. comm-mode = None? is not the right option for disabling com motion removal)?

If it's the former case I believe it would be more user-friendly not to show the note in case the simulation involves position restraints AND no com motion removal.


Thanks.


Regards,

Michele

From dallas.warren at monash.edu  Tue Jan 28 21:34:55 2020
From: dallas.warren at monash.edu (Dallas Warren)
Date: Tue, 28 Jan 2020 20:34:55 -0000
Subject: [gmx-users] DNA-Protein complex
In-Reply-To: <CACD+=T9i++YFG17UrBFW2=UtvjYmEd3x5HS8ErJnvCHt8=6kXg@mail.gmail.com>
References: <CACD+=T9i++YFG17UrBFW2=UtvjYmEd3x5HS8ErJnvCHt8=6kXg@mail.gmail.com>
Message-ID: <CAOv1qzaqiq9==1qmni6owaEU+UN9btBwGY2dqCJ=gFY9zCLmdQ@mail.gmail.com>

Check the literature to see what others that are simulating similar
molecules are using and looking to study similar "things" (energies,
structures etc) that you are.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Wed, 29 Jan 2020 at 00:53, Rakesh Bhowmick <inforak.007 at gmail.com> wrote:

> I am new in the field of molecular dynamics and simulation. I am trying to
> learn online tutorial for gromacs. I have docked my DNA with protein in
> HADDOCK. I want to run a simulation in gromacs. Can I make topology file of
> the complex together or I need to make topology file separately. Which
> forcefield should I use for DNA protein complex?
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From rlwoltz at ucdavis.edu  Wed Jan 29 00:14:04 2020
From: rlwoltz at ucdavis.edu (Ryan Woltz)
Date: Tue, 28 Jan 2020 23:14:04 -0000
Subject: [gmx-users] gromacs-2020 build gcc/nvcc error
Message-ID: <CADvvA5TGm+YnTiRPBi3WNqyKaGwQZdvA2M0Yoep-6tEDdQuQUA@mail.gmail.com>

Hello Gromacs experts,

          First things first, I apologize for any double post but I just
joined the community so I'm very new and only found 1-2 posts related to my
problem but the solutions did not work. I have been doing MD for about
6-months using NAMD but want to also try out Gromacs. That being said I am
slightly familiar with CPU modeling programs like Rosetta, but I am totally
lost when it comes to fixing errors using GPU accelerated code for CUDA. I
did find that at one point my error was fixed for an earlier version of
Gromacs but Gromacs-2020 may have resurfaced the same error again, here is
what I think my error is:

https://redmine.gromacs.org/issues/1982

    I am running Ubuntu 18.04.03 LTS, and gromacs-2020 I did initially have
the gcc/nvcc incompatible but I think installing and using gcc-5/g++-5
version command in cmake has fixed that issue. I have a NVIDIA card with
CUDA-9.1 driver when I type nvcc --version.

my cmake command is as follows:

CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
-DGMX_GPLUSPLUS_PATH=/usr/bin/g++-5 -DCUDA_HOST_COMPILER=gcc-5
-DCMAKE_CXX_COMPILER=g++-5 -DCMAKE_C_COMPILER=/usr/bin/gcc-5
-DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug (I did
try adding -D_FORCE_INLINES= based on the link above in my running command
but it did not work). I did look at the error log but it is way over my
head. I have in addition deleted the CMakeCache.txt file or the unpacked
Gromacs and re-unzipped it to restart the cmake process to make sure it was
starting "clean". Is there any additional information I could provide? Does
anyone have a suggestion? Again I'm sorry if this is a duplicate,
everything I found on other sites was way over my head and I generally
understand what is going on but the forums I read on possible solutions
seem way over my head and I'm afraid I will break the driver if I attempt
them (which has happened to me already and the computer required a full
reinstall).

here is last lines from the build:

-- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable
version "1.11.6", minimum required is "1.5")
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Adding work-around for issue compiling CUDA code with glibc 2.23 string.h
-- Check for working NVCC/C++ compiler combination with nvcc
'/usr/local/cuda/bin/nvcc'
-- Check for working NVCC/C compiler combination - broken
-- /usr/local/cuda/bin/nvcc standard output: ''
-- /usr/local/cuda/bin/nvcc standard error:
 '/home/rlwoltz/protein_modeling/gromacs-2020/build/gcc-5: No such file or
directory
'
CMake Error at cmake/gmxManageNvccConfig.cmake:189 (message):
  CUDA compiler does not seem to be functional.
Call Stack (most recent call first):
  cmake/gmxManageGPU.cmake:207 (include)
  CMakeLists.txt:577 (gmx_gpu_setup)


-- Configuring incomplete, errors occurred!
See also
"/home/rlwoltz/protein_modeling/gromacs-2020/build/CMakeFiles/CMakeOutput.log".
See also
"/home/rlwoltz/protein_modeling/gromacs-2020/build/CMakeFiles/CMakeError.log".

From aayattimg at bose.res.in  Wed Jan 29 08:20:08 2020
From: aayattimg at bose.res.in (aayattimg at bose.res.in)
Date: Wed, 29 Jan 2020 07:20:08 -0000
Subject: [gmx-users] DNA-Protein complex
In-Reply-To: <CAOv1qzaqiq9==1qmni6owaEU+UN9btBwGY2dqCJ=gFY9zCLmdQ@mail.gmail.com>
References: <CACD+=T9i++YFG17UrBFW2=UtvjYmEd3x5HS8ErJnvCHt8=6kXg@mail.gmail.com>
	<CAOv1qzaqiq9==1qmni6owaEU+UN9btBwGY2dqCJ=gFY9zCLmdQ@mail.gmail.com>
Message-ID: <52026.103.230.166.2.1580280592.squirrel@bose.res.in>

> I think you don`t need to build topology separately. Using appropriate
force field will do. For protein-DNA simulation amber99sb works well.
Amber99bsc1.ff is a new module available for gromacs users. You may use
them or it is always better to refer literature to use the more
appropriate forcefeild.
Good Luck!
Check the literature to see what others that are simulating similar
> molecules are using and looking to study similar "things" (energies,
> structures etc) that you are.
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren at monash.edu
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On Wed, 29 Jan 2020 at 00:53, Rakesh Bhowmick <inforak.007 at gmail.com>
> wrote:
>
>> I am new in the field of molecular dynamics and simulation. I am trying
>> to
>> learn online tutorial for gromacs. I have docked my DNA with protein in
>> HADDOCK. I want to run a simulation in gromacs. Can I make topology file
>> of
>> the complex together or I need to make topology file separately. Which
>> forcefield should I use for DNA protein complex?
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
> a mail to gmx-users-request at gromacs.org.
>


From pall.szilard at gmail.com  Wed Jan 29 11:05:43 2020
From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=)
Date: Wed, 29 Jan 2020 10:05:43 -0000
Subject: [gmx-users] gromacs-2020 build gcc/nvcc error
In-Reply-To: <CADvvA5TGm+YnTiRPBi3WNqyKaGwQZdvA2M0Yoep-6tEDdQuQUA@mail.gmail.com>
References: <CADvvA5TGm+YnTiRPBi3WNqyKaGwQZdvA2M0Yoep-6tEDdQuQUA@mail.gmail.com>
Message-ID: <CANnYEw7GOiPgL0F2cBuSpZKPWUZ=McBYL4TVJkNrWOVS613M9g@mail.gmail.com>

Hi Ryan,

The issue you linked has been worked around in the build system, so my
guess is that the issue you are seeing is not related.

I would recommend that you update your software stack to the latest version
(both CUDA 9.1 and gcc 5 are a few years old). On Ubuntu 18.04 you should
be able to get gcc 8 through the package manager. Together with
upgrading to the latest CUDA might well solve your issues.

Let us know if that worked!

Cheers,
--
Szil?rd


On Wed, Jan 29, 2020 at 12:14 AM Ryan Woltz <rlwoltz at ucdavis.edu> wrote:

> Hello Gromacs experts,
>
>           First things first, I apologize for any double post but I just
> joined the community so I'm very new and only found 1-2 posts related to my
> problem but the solutions did not work. I have been doing MD for about
> 6-months using NAMD but want to also try out Gromacs. That being said I am
> slightly familiar with CPU modeling programs like Rosetta, but I am totally
> lost when it comes to fixing errors using GPU accelerated code for CUDA. I
> did find that at one point my error was fixed for an earlier version of
> Gromacs but Gromacs-2020 may have resurfaced the same error again, here is
> what I think my error is:
>
> https://redmine.gromacs.org/issues/1982
>
>     I am running Ubuntu 18.04.03 LTS, and gromacs-2020 I did initially have
> the gcc/nvcc incompatible but I think installing and using gcc-5/g++-5
> version command in cmake has fixed that issue. I have a NVIDIA card with
> CUDA-9.1 driver when I type nvcc --version.
>
> my cmake command is as follows:
>
> CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
> -DGMX_GPLUSPLUS_PATH=/usr/bin/g++-5 -DCUDA_HOST_COMPILER=gcc-5
> -DCMAKE_CXX_COMPILER=g++-5 -DCMAKE_C_COMPILER=/usr/bin/gcc-5
> -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug (I did
> try adding -D_FORCE_INLINES= based on the link above in my running command
> but it did not work). I did look at the error log but it is way over my
> head. I have in addition deleted the CMakeCache.txt file or the unpacked
> Gromacs and re-unzipped it to restart the cmake process to make sure it was
> starting "clean". Is there any additional information I could provide? Does
> anyone have a suggestion? Again I'm sorry if this is a duplicate,
> everything I found on other sites was way over my head and I generally
> understand what is going on but the forums I read on possible solutions
> seem way over my head and I'm afraid I will break the driver if I attempt
> them (which has happened to me already and the computer required a full
> reinstall).
>
> here is last lines from the build:
>
> -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable
> version "1.11.6", minimum required is "1.5")
> -- Looking for C++ include pthread.h
> -- Looking for C++ include pthread.h - found
> -- Atomic operations found
> -- Performing Test PTHREAD_SETAFFINITY
> -- Performing Test PTHREAD_SETAFFINITY - Success
> -- Adding work-around for issue compiling CUDA code with glibc 2.23
> string.h
> -- Check for working NVCC/C++ compiler combination with nvcc
> '/usr/local/cuda/bin/nvcc'
> -- Check for working NVCC/C compiler combination - broken
> -- /usr/local/cuda/bin/nvcc standard output: ''
> -- /usr/local/cuda/bin/nvcc standard error:
>  '/home/rlwoltz/protein_modeling/gromacs-2020/build/gcc-5: No such file or
> directory
> '
> CMake Error at cmake/gmxManageNvccConfig.cmake:189 (message):
>   CUDA compiler does not seem to be functional.
> Call Stack (most recent call first):
>   cmake/gmxManageGPU.cmake:207 (include)
>   CMakeLists.txt:577 (gmx_gpu_setup)
>
>
> -- Configuring incomplete, errors occurred!
> See also
>
> "/home/rlwoltz/protein_modeling/gromacs-2020/build/CMakeFiles/CMakeOutput.log".
> See also
>
> "/home/rlwoltz/protein_modeling/gromacs-2020/build/CMakeFiles/CMakeError.log".
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From pall.szilard at gmail.com  Wed Jan 29 11:05:43 2020
From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=)
Date: Wed, 29 Jan 2020 10:05:43 -0000
Subject: [gmx-users] gromacs-2020 build gcc/nvcc error
In-Reply-To: <CADvvA5TGm+YnTiRPBi3WNqyKaGwQZdvA2M0Yoep-6tEDdQuQUA@mail.gmail.com>
References: <CADvvA5TGm+YnTiRPBi3WNqyKaGwQZdvA2M0Yoep-6tEDdQuQUA@mail.gmail.com>
Message-ID: <CANnYEw7GOiPgL0F2cBuSpZKPWUZ=McBYL4TVJkNrWOVS613M9g@mail.gmail.com>

Hi Ryan,

The issue you linked has been worked around in the build system, so my
guess is that the issue you are seeing is not related.

I would recommend that you update your software stack to the latest version
(both CUDA 9.1 and gcc 5 are a few years old). On Ubuntu 18.04 you should
be able to get gcc 8 through the package manager. Together with
upgrading to the latest CUDA might well solve your issues.

Let us know if that worked!

Cheers,
--
Szil?rd


On Wed, Jan 29, 2020 at 12:14 AM Ryan Woltz <rlwoltz at ucdavis.edu> wrote:

> Hello Gromacs experts,
>
>           First things first, I apologize for any double post but I just
> joined the community so I'm very new and only found 1-2 posts related to my
> problem but the solutions did not work. I have been doing MD for about
> 6-months using NAMD but want to also try out Gromacs. That being said I am
> slightly familiar with CPU modeling programs like Rosetta, but I am totally
> lost when it comes to fixing errors using GPU accelerated code for CUDA. I
> did find that at one point my error was fixed for an earlier version of
> Gromacs but Gromacs-2020 may have resurfaced the same error again, here is
> what I think my error is:
>
> https://redmine.gromacs.org/issues/1982
>
>     I am running Ubuntu 18.04.03 LTS, and gromacs-2020 I did initially have
> the gcc/nvcc incompatible but I think installing and using gcc-5/g++-5
> version command in cmake has fixed that issue. I have a NVIDIA card with
> CUDA-9.1 driver when I type nvcc --version.
>
> my cmake command is as follows:
>
> CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
> -DGMX_GPLUSPLUS_PATH=/usr/bin/g++-5 -DCUDA_HOST_COMPILER=gcc-5
> -DCMAKE_CXX_COMPILER=g++-5 -DCMAKE_C_COMPILER=/usr/bin/gcc-5
> -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug (I did
> try adding -D_FORCE_INLINES= based on the link above in my running command
> but it did not work). I did look at the error log but it is way over my
> head. I have in addition deleted the CMakeCache.txt file or the unpacked
> Gromacs and re-unzipped it to restart the cmake process to make sure it was
> starting "clean". Is there any additional information I could provide? Does
> anyone have a suggestion? Again I'm sorry if this is a duplicate,
> everything I found on other sites was way over my head and I generally
> understand what is going on but the forums I read on possible solutions
> seem way over my head and I'm afraid I will break the driver if I attempt
> them (which has happened to me already and the computer required a full
> reinstall).
>
> here is last lines from the build:
>
> -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable
> version "1.11.6", minimum required is "1.5")
> -- Looking for C++ include pthread.h
> -- Looking for C++ include pthread.h - found
> -- Atomic operations found
> -- Performing Test PTHREAD_SETAFFINITY
> -- Performing Test PTHREAD_SETAFFINITY - Success
> -- Adding work-around for issue compiling CUDA code with glibc 2.23
> string.h
> -- Check for working NVCC/C++ compiler combination with nvcc
> '/usr/local/cuda/bin/nvcc'
> -- Check for working NVCC/C compiler combination - broken
> -- /usr/local/cuda/bin/nvcc standard output: ''
> -- /usr/local/cuda/bin/nvcc standard error:
>  '/home/rlwoltz/protein_modeling/gromacs-2020/build/gcc-5: No such file or
> directory
> '
> CMake Error at cmake/gmxManageNvccConfig.cmake:189 (message):
>   CUDA compiler does not seem to be functional.
> Call Stack (most recent call first):
>   cmake/gmxManageGPU.cmake:207 (include)
>   CMakeLists.txt:577 (gmx_gpu_setup)
>
>
> -- Configuring incomplete, errors occurred!
> See also
>
> "/home/rlwoltz/protein_modeling/gromacs-2020/build/CMakeFiles/CMakeOutput.log".
> See also
>
> "/home/rlwoltz/protein_modeling/gromacs-2020/build/CMakeFiles/CMakeError.log".
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From asakshi1996 at gmail.com  Wed Jan 29 12:05:28 2020
From: asakshi1996 at gmail.com (Sakshi Arora)
Date: Wed, 29 Jan 2020 11:05:28 -0000
Subject: [gmx-users] ERROR DURING INSTALLATION
Message-ID: <CAKwqCnFtwCEpU8nMN7Da4CHwbD+sH+LA1QPhxxDMxsLVBuSpDw@mail.gmail.com>

I am using Linux to install gromacs and have installed all the
prerequisites and programs and packages as per my knowledge. In the build
directory, after using the command - 'cmake ..' I have received the
following error message. Please help me out with this.
ERROR -
CMake Error at CMakeLists.txt:63 (include):
  include could not find load file:
    gmxManageCcache
CMake Warning at CMakeLists.txt:69 (find_package):
  By not providing "FindLibStdCpp.cmake" in CMAKE_MODULE_PATH this project
  has asked CMake to find a package configuration file provided by
  "LibStdCpp", but CMake did not find one.
  Could not find a package configuration file provided by "LibStdCpp" with
  any of the following names:
    LibStdCppConfig.cmake
    libstdcpp-config.cmake
  Add the installation prefix of "LibStdCpp" to CMAKE_PREFIX_PATH or set
  "LibStdCpp_DIR" to a directory containing one of the above files.  If
  "LibStdCpp" provides a separate development package or SDK, be sure it has
  been installed.
CMake Error at CMakeLists.txt:75 (include):
  include could not find load file:
    gmxBuildTreeInfo
CMake Error at CMakeLists.txt:76 (include):
  include could not find load file:
    gmxVersionInfo
CMake Error at CMakeLists.txt:85 (include):
  include could not find load file:
    gmxBuildTypeReference
CMake Error at CMakeLists.txt:86 (include):
  include could not find load file:
    gmxBuildTypeProfile
CMake Error at CMakeLists.txt:87 (include):
  include could not find load file:
    gmxBuildTypeTSAN
CMake Error at CMakeLists.txt:88 (include):
  include could not find load file:
    gmxBuildTypeASAN
CMake Error at CMakeLists.txt:89 (include):
  include could not find load file:
    gmxBuildTypeMSAN
CMake Error at CMakeLists.txt:90 (include):
  include could not find load file:
    gmxBuildTypeReleaseWithAssert
CMake Error at CMakeLists.txt:112 (include):
  include could not find load file:
    gmxCTestUtilities
CMake Error at CMakeLists.txt:113 (gmx_ctest_init):
  Unknown CMake command "gmx_ctest_init".
-- Configuring incomplete, errors occurred!
See also "/home/sakshi/Downloads/gromacs-2020/CMakeFiles/CMakeOutput.log".\
Regards,
Sakshi Arora

From anusharma.jan1995 at gmail.com  Wed Jan 29 16:20:21 2020
From: anusharma.jan1995 at gmail.com (anupama sharma)
Date: Wed, 29 Jan 2020 15:20:21 -0000
Subject: [gmx-users] gmx dens charge
Message-ID: <CABhH7Kn11D2DHjbMRRqi7kVmGz06WyrQpgPcWRgs6vMPE-tgbw@mail.gmail.com>

Dear users,
I need to know for charge density calculation specially for water, should
we use -center /-symm option or not and if not why?
Since I tried the option (-center/-symm) for charge density calculation of
water and gmx dens module was not reading frame. I used the gromacs version
5.1.4 for the analysis.
I will be highly thankful if any one can suggest me regarding this.

From franklam66 at gmail.com  Wed Jan 29 20:55:40 2020
From: franklam66 at gmail.com (Frank Lam)
Date: Wed, 29 Jan 2020 19:55:40 -0000
Subject: [gmx-users] Cell Membrane Potential
Message-ID: <CAMC9dP-jycq_Y2g4RTbLZBMh0KErfbba2DAugzsbSLthPZ=cJg@mail.gmail.com>

Hi,

I am undergraduate student wanting to learn and use GROMACS for a project
on membrane proteins. Is altering membrane potential in a simulation
possible using GROMACS? I do apologize if this is trivial. I tried looking
at the documentation, but most of the information are currently too
challenging for me. Any guidance would be greatly appreciated.

kind regards,
Frank

From rlwoltz at ucdavis.edu  Wed Jan 29 22:34:49 2020
From: rlwoltz at ucdavis.edu (Ryan Woltz)
Date: Wed, 29 Jan 2020 21:34:49 -0000
Subject: [gmx-users] gromacs-2020 build gcc/nvcc error
In-Reply-To: <CANnYEw7GOiPgL0F2cBuSpZKPWUZ=McBYL4TVJkNrWOVS613M9g@mail.gmail.com>
References: <CADvvA5TGm+YnTiRPBi3WNqyKaGwQZdvA2M0Yoep-6tEDdQuQUA@mail.gmail.com>
	<CANnYEw7GOiPgL0F2cBuSpZKPWUZ=McBYL4TVJkNrWOVS613M9g@mail.gmail.com>
Message-ID: <CADvvA5Tj5UYYxyiDH0XN2UE12jYBJGpLhbC0GpJVLaBG2cr_kA@mail.gmail.com>

Dear Szil?rd,

         Thank you for your quick response. You are correct, after
issuing sudo apt-get install gcc-9 g++-9 CMake was run with:

CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ -DGMX_BUILD_OWN_FFTW=ON
-DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug

However now I'm getting an error in make

make VERBOSE=1

error:

[ 25%] Building CXX object
src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o
In file included from
/home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512.h:46:0,
                 from
/home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/simd.h:146,
                 from
/home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/nbnxm_simd.h:40,
                 from
/home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp:49:
/home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:
In function ?void gmx::gatherLoadTransposeHsimd(const float*, const float*,
const int32_t*, gmx::SimdFloat*, gmx::SimdFloat*) [with int align = 2;
int32_t = int]?:
/home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:422:28:
error: the last argument must be scale 1, 2, 4, 8
     tmp1 = _mm512_castpd_ps(
                            ^
/home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:424:28:
error: the last argument must be scale 1, 2, 4, 8
     tmp2 = _mm512_castpd_ps(
                            ^
src/gromacs/CMakeFiles/libgromacs.dir/build.make:13881: recipe for target
'src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o'
failed
make[2]: ***
[src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o]
Error 1
CMakeFiles/Makefile2:2910: recipe for target
'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
Makefile:162: recipe for target 'all' failed
make: *** [all] Error 2

after doing a 1 hour google I found discussions saying that the error
(Makefile:162: recipe for target 'all' failed) is too vague with no general
solution. I found fixes for headers and other files for other programs but
not fixes for this file. The fix linked below is for gromacs-2018 and a
different file but the general problem seems to suggest it still is a
gcc/g++ version compatibility error correct? Any suggestions for this error?

https://redmine.gromacs.org/issues/2312


Thank you so much,

Ryan

 PS Just to document for anyone else going through what I did for
Gromacs-2020 these were my steps.

sudo apt-get install gcc g++
cmake ../ -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON

 I then received multiple errors complaining about nvcc/C++
incompatibility. After researching found errors for previous gromacs
versions suggesting to use gcc-5 (but as you suggested this error has been
patched).

sudo apt-get install gcc-5 g++-5
CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
-DGMX_GPLUSPLUS_PATH=/usr/bin/g++-5 -DCUDA_HOST_COMPILER=gcc-5
-DCMAKE_CXX_COMPILER=g++-5 -DCMAKE_C_COMPILER=/usr/bin/gcc-5
-DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug
-D_FORCE_INLINES=OFF

Received different error described in previous email and solved with your
suggested solution. The key might be to specifically install latest version
number i.e.

sudo apt-get install gcc-X g++-X (with X being the largest number
available).




On Wed, Jan 29, 2020 at 2:05 AM Szil?rd P?ll <pall.szilard at gmail.com> wrote:

> Hi Ryan,
>
> The issue you linked has been worked around in the build system, so my
> guess is that the issue you are seeing is not related.
>
> I would recommend that you update your software stack to the latest version
> (both CUDA 9.1 and gcc 5 are a few years old). On Ubuntu 18.04 you should
> be able to get gcc 8 through the package manager. Together with
> upgrading to the latest CUDA might well solve your issues.
>
> Let us know if that worked!
>
> Cheers,
> --
> Szil?rd
>
>
> On Wed, Jan 29, 2020 at 12:14 AM Ryan Woltz <rlwoltz at ucdavis.edu> wrote:
>
> > Hello Gromacs experts,
> >
> >           First things first, I apologize for any double post but I just
> > joined the community so I'm very new and only found 1-2 posts related to
> my
> > problem but the solutions did not work. I have been doing MD for about
> > 6-months using NAMD but want to also try out Gromacs. That being said I
> am
> > slightly familiar with CPU modeling programs like Rosetta, but I am
> totally
> > lost when it comes to fixing errors using GPU accelerated code for CUDA.
> I
> > did find that at one point my error was fixed for an earlier version of
> > Gromacs but Gromacs-2020 may have resurfaced the same error again, here
> is
> > what I think my error is:
> >
> > https://redmine.gromacs.org/issues/1982
> >
> >     I am running Ubuntu 18.04.03 LTS, and gromacs-2020 I did initially
> have
> > the gcc/nvcc incompatible but I think installing and using gcc-5/g++-5
> > version command in cmake has fixed that issue. I have a NVIDIA card with
> > CUDA-9.1 driver when I type nvcc --version.
> >
> > my cmake command is as follows:
> >
> > CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
> > -DGMX_GPLUSPLUS_PATH=/usr/bin/g++-5 -DCUDA_HOST_COMPILER=gcc-5
> > -DCMAKE_CXX_COMPILER=g++-5 -DCMAKE_C_COMPILER=/usr/bin/gcc-5
> > -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug (I did
> > try adding -D_FORCE_INLINES= based on the link above in my running
> command
> > but it did not work). I did look at the error log but it is way over my
> > head. I have in addition deleted the CMakeCache.txt file or the unpacked
> > Gromacs and re-unzipped it to restart the cmake process to make sure it
> was
> > starting "clean". Is there any additional information I could provide?
> Does
> > anyone have a suggestion? Again I'm sorry if this is a duplicate,
> > everything I found on other sites was way over my head and I generally
> > understand what is going on but the forums I read on possible solutions
> > seem way over my head and I'm afraid I will break the driver if I attempt
> > them (which has happened to me already and the computer required a full
> > reinstall).
> >
> > here is last lines from the build:
> >
> > -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable
> > version "1.11.6", minimum required is "1.5")
> > -- Looking for C++ include pthread.h
> > -- Looking for C++ include pthread.h - found
> > -- Atomic operations found
> > -- Performing Test PTHREAD_SETAFFINITY
> > -- Performing Test PTHREAD_SETAFFINITY - Success
> > -- Adding work-around for issue compiling CUDA code with glibc 2.23
> > string.h
> > -- Check for working NVCC/C++ compiler combination with nvcc
> > '/usr/local/cuda/bin/nvcc'
> > -- Check for working NVCC/C compiler combination - broken
> > -- /usr/local/cuda/bin/nvcc standard output: ''
> > -- /usr/local/cuda/bin/nvcc standard error:
> >  '/home/rlwoltz/protein_modeling/gromacs-2020/build/gcc-5: No such file
> or
> > directory
> > '
> > CMake Error at cmake/gmxManageNvccConfig.cmake:189 (message):
> >   CUDA compiler does not seem to be functional.
> > Call Stack (most recent call first):
> >   cmake/gmxManageGPU.cmake:207 (include)
> >   CMakeLists.txt:577 (gmx_gpu_setup)
> >
> >
> > -- Configuring incomplete, errors occurred!
> > See also
> >
> >
> "/home/rlwoltz/protein_modeling/gromacs-2020/build/CMakeFiles/CMakeOutput.log".
> > See also
> >
> >
> "/home/rlwoltz/protein_modeling/gromacs-2020/build/CMakeFiles/CMakeError.log".
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

From rlwoltz at ucdavis.edu  Wed Jan 29 22:34:49 2020
From: rlwoltz at ucdavis.edu (Ryan Woltz)
Date: Wed, 29 Jan 2020 21:34:49 -0000
Subject: [gmx-users] gromacs-2020 build gcc/nvcc error
In-Reply-To: <CANnYEw7GOiPgL0F2cBuSpZKPWUZ=McBYL4TVJkNrWOVS613M9g@mail.gmail.com>
References: <CADvvA5TGm+YnTiRPBi3WNqyKaGwQZdvA2M0Yoep-6tEDdQuQUA@mail.gmail.com>
	<CANnYEw7GOiPgL0F2cBuSpZKPWUZ=McBYL4TVJkNrWOVS613M9g@mail.gmail.com>
Message-ID: <CADvvA5Tj5UYYxyiDH0XN2UE12jYBJGpLhbC0GpJVLaBG2cr_kA@mail.gmail.com>

Dear Szil?rd,

         Thank you for your quick response. You are correct, after
issuing sudo apt-get install gcc-9 g++-9 CMake was run with:

CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ -DGMX_BUILD_OWN_FFTW=ON
-DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug

However now I'm getting an error in make

make VERBOSE=1

error:

[ 25%] Building CXX object
src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o
In file included from
/home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512.h:46:0,
                 from
/home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/simd.h:146,
                 from
/home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/nbnxm_simd.h:40,
                 from
/home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp:49:
/home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:
In function ?void gmx::gatherLoadTransposeHsimd(const float*, const float*,
const int32_t*, gmx::SimdFloat*, gmx::SimdFloat*) [with int align = 2;
int32_t = int]?:
/home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:422:28:
error: the last argument must be scale 1, 2, 4, 8
     tmp1 = _mm512_castpd_ps(
                            ^
/home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:424:28:
error: the last argument must be scale 1, 2, 4, 8
     tmp2 = _mm512_castpd_ps(
                            ^
src/gromacs/CMakeFiles/libgromacs.dir/build.make:13881: recipe for target
'src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o'
failed
make[2]: ***
[src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o]
Error 1
CMakeFiles/Makefile2:2910: recipe for target
'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
Makefile:162: recipe for target 'all' failed
make: *** [all] Error 2

after doing a 1 hour google I found discussions saying that the error
(Makefile:162: recipe for target 'all' failed) is too vague with no general
solution. I found fixes for headers and other files for other programs but
not fixes for this file. The fix linked below is for gromacs-2018 and a
different file but the general problem seems to suggest it still is a
gcc/g++ version compatibility error correct? Any suggestions for this error?

https://redmine.gromacs.org/issues/2312


Thank you so much,

Ryan

 PS Just to document for anyone else going through what I did for
Gromacs-2020 these were my steps.

sudo apt-get install gcc g++
cmake ../ -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON

 I then received multiple errors complaining about nvcc/C++
incompatibility. After researching found errors for previous gromacs
versions suggesting to use gcc-5 (but as you suggested this error has been
patched).

sudo apt-get install gcc-5 g++-5
CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
-DGMX_GPLUSPLUS_PATH=/usr/bin/g++-5 -DCUDA_HOST_COMPILER=gcc-5
-DCMAKE_CXX_COMPILER=g++-5 -DCMAKE_C_COMPILER=/usr/bin/gcc-5
-DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug
-D_FORCE_INLINES=OFF

Received different error described in previous email and solved with your
suggested solution. The key might be to specifically install latest version
number i.e.

sudo apt-get install gcc-X g++-X (with X being the largest number
available).




On Wed, Jan 29, 2020 at 2:05 AM Szil?rd P?ll <pall.szilard at gmail.com> wrote:

> Hi Ryan,
>
> The issue you linked has been worked around in the build system, so my
> guess is that the issue you are seeing is not related.
>
> I would recommend that you update your software stack to the latest version
> (both CUDA 9.1 and gcc 5 are a few years old). On Ubuntu 18.04 you should
> be able to get gcc 8 through the package manager. Together with
> upgrading to the latest CUDA might well solve your issues.
>
> Let us know if that worked!
>
> Cheers,
> --
> Szil?rd
>
>
> On Wed, Jan 29, 2020 at 12:14 AM Ryan Woltz <rlwoltz at ucdavis.edu> wrote:
>
> > Hello Gromacs experts,
> >
> >           First things first, I apologize for any double post but I just
> > joined the community so I'm very new and only found 1-2 posts related to
> my
> > problem but the solutions did not work. I have been doing MD for about
> > 6-months using NAMD but want to also try out Gromacs. That being said I
> am
> > slightly familiar with CPU modeling programs like Rosetta, but I am
> totally
> > lost when it comes to fixing errors using GPU accelerated code for CUDA.
> I
> > did find that at one point my error was fixed for an earlier version of
> > Gromacs but Gromacs-2020 may have resurfaced the same error again, here
> is
> > what I think my error is:
> >
> > https://redmine.gromacs.org/issues/1982
> >
> >     I am running Ubuntu 18.04.03 LTS, and gromacs-2020 I did initially
> have
> > the gcc/nvcc incompatible but I think installing and using gcc-5/g++-5
> > version command in cmake has fixed that issue. I have a NVIDIA card with
> > CUDA-9.1 driver when I type nvcc --version.
> >
> > my cmake command is as follows:
> >
> > CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
> > -DGMX_GPLUSPLUS_PATH=/usr/bin/g++-5 -DCUDA_HOST_COMPILER=gcc-5
> > -DCMAKE_CXX_COMPILER=g++-5 -DCMAKE_C_COMPILER=/usr/bin/gcc-5
> > -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug (I did
> > try adding -D_FORCE_INLINES= based on the link above in my running
> command
> > but it did not work). I did look at the error log but it is way over my
> > head. I have in addition deleted the CMakeCache.txt file or the unpacked
> > Gromacs and re-unzipped it to restart the cmake process to make sure it
> was
> > starting "clean". Is there any additional information I could provide?
> Does
> > anyone have a suggestion? Again I'm sorry if this is a duplicate,
> > everything I found on other sites was way over my head and I generally
> > understand what is going on but the forums I read on possible solutions
> > seem way over my head and I'm afraid I will break the driver if I attempt
> > them (which has happened to me already and the computer required a full
> > reinstall).
> >
> > here is last lines from the build:
> >
> > -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable
> > version "1.11.6", minimum required is "1.5")
> > -- Looking for C++ include pthread.h
> > -- Looking for C++ include pthread.h - found
> > -- Atomic operations found
> > -- Performing Test PTHREAD_SETAFFINITY
> > -- Performing Test PTHREAD_SETAFFINITY - Success
> > -- Adding work-around for issue compiling CUDA code with glibc 2.23
> > string.h
> > -- Check for working NVCC/C++ compiler combination with nvcc
> > '/usr/local/cuda/bin/nvcc'
> > -- Check for working NVCC/C compiler combination - broken
> > -- /usr/local/cuda/bin/nvcc standard output: ''
> > -- /usr/local/cuda/bin/nvcc standard error:
> >  '/home/rlwoltz/protein_modeling/gromacs-2020/build/gcc-5: No such file
> or
> > directory
> > '
> > CMake Error at cmake/gmxManageNvccConfig.cmake:189 (message):
> >   CUDA compiler does not seem to be functional.
> > Call Stack (most recent call first):
> >   cmake/gmxManageGPU.cmake:207 (include)
> >   CMakeLists.txt:577 (gmx_gpu_setup)
> >
> >
> > -- Configuring incomplete, errors occurred!
> > See also
> >
> >
> "/home/rlwoltz/protein_modeling/gromacs-2020/build/CMakeFiles/CMakeOutput.log".
> > See also
> >
> >
> "/home/rlwoltz/protein_modeling/gromacs-2020/build/CMakeFiles/CMakeError.log".
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

From mbhendle at iitk.ac.in  Thu Jan 30 10:26:08 2020
From: mbhendle at iitk.ac.in (mbhendle)
Date: Thu, 30 Jan 2020 09:26:08 -0000
Subject: [gmx-users] How to use TIP4P-ICE water model
Message-ID: <1eef5fd039bdc2cd0c256d2dc33abcf0@iitk.ac.in>

Dear all, 

I want to use TIP4P-ICE water model for my simulations, but inbuilt .gro
file of TIP4P-ICE is not available in Gromacs 2018. I tried alternate
method by solvating using TIP4P model and then by changing the "itp"
file of TIP4P in topology file with that of TIP4P-ICE. 

But the result of this simulation(RDF) is very different from that of
literature. Please suggest any alternate approach. 

Thanks & Regards, 

Mangesh Bhendale

From alessandra.villa.biosim at gmail.com  Thu Jan 30 11:40:30 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Thu, 30 Jan 2020 10:40:30 -0000
Subject: [gmx-users] TraPPE-EH in GROMACS
In-Reply-To: <CACrPy4Cmb2qD4Wo+XTZALDgQ_+5Y5Zg2FguDdZf7sxoEKe_4AA@mail.gmail.com>
References: <CACrPy4Cmb2qD4Wo+XTZALDgQ_+5Y5Zg2FguDdZf7sxoEKe_4AA@mail.gmail.com>
Message-ID: <CANogp5xtUJ+bEp59htGKbeSmgvXT4Nzn4fLoZtpKfTmzSb4G_Q@mail.gmail.com>

Hi
Maybe the definitions in the manual page (middle part) below may help you.
(
http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html?highlight=file%20top
)
Best regards
Alessandra

On Tue, Jan 28, 2020 at 8:41 AM Dhrubajyoti Maji <dmaji43 at gmail.com> wrote:

> Dear gromacs users,
>         I want to use TraPPE-EH force field parameters in GROMACS-2018.3. I
> have understood that in top file nbfunc=1,
> comb-rule=2,fudgeLJ=0.5,fudgeQQ=0.8333. But what will be the values of
> gen-pairs, nrexcl and [ pairs] section ? Any kind of help will be highly
> appreciated.
> Thanks and regards
>
> Dhrubajyoti Maji
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Thu Jan 30 11:40:30 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Thu, 30 Jan 2020 10:40:30 -0000
Subject: [gmx-users] TraPPE-EH in GROMACS
In-Reply-To: <CACrPy4Cmb2qD4Wo+XTZALDgQ_+5Y5Zg2FguDdZf7sxoEKe_4AA@mail.gmail.com>
References: <CACrPy4Cmb2qD4Wo+XTZALDgQ_+5Y5Zg2FguDdZf7sxoEKe_4AA@mail.gmail.com>
Message-ID: <CANogp5xtUJ+bEp59htGKbeSmgvXT4Nzn4fLoZtpKfTmzSb4G_Q@mail.gmail.com>

Hi
Maybe the definitions in the manual page (middle part) below may help you.
(
http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html?highlight=file%20top
)
Best regards
Alessandra

On Tue, Jan 28, 2020 at 8:41 AM Dhrubajyoti Maji <dmaji43 at gmail.com> wrote:

> Dear gromacs users,
>         I want to use TraPPE-EH force field parameters in GROMACS-2018.3. I
> have understood that in top file nbfunc=1,
> comb-rule=2,fudgeLJ=0.5,fudgeQQ=0.8333. But what will be the values of
> gen-pairs, nrexcl and [ pairs] section ? Any kind of help will be highly
> appreciated.
> Thanks and regards
>
> Dhrubajyoti Maji
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From pall.szilard at gmail.com  Thu Jan 30 14:50:34 2020
From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=)
Date: Thu, 30 Jan 2020 13:50:34 -0000
Subject: [gmx-users] gromacs-2020 build gcc/nvcc error
In-Reply-To: <CADvvA5Tj5UYYxyiDH0XN2UE12jYBJGpLhbC0GpJVLaBG2cr_kA@mail.gmail.com>
References: <CADvvA5TGm+YnTiRPBi3WNqyKaGwQZdvA2M0Yoep-6tEDdQuQUA@mail.gmail.com>
	<CANnYEw7GOiPgL0F2cBuSpZKPWUZ=McBYL4TVJkNrWOVS613M9g@mail.gmail.com>
	<CADvvA5Tj5UYYxyiDH0XN2UE12jYBJGpLhbC0GpJVLaBG2cr_kA@mail.gmail.com>
Message-ID: <CANnYEw7exAJWpe5J-Jx8AmytJTxgGz3xnM9qXJj_NPodfhEzow@mail.gmail.com>

Dear Ryan,

On Wed, Jan 29, 2020 at 10:35 PM Ryan Woltz <rlwoltz at ucdavis.edu> wrote:

> Dear Szil?rd,
>
>          Thank you for your quick response. You are correct, after
> issuing sudo apt-get install gcc-9 g++-9 CMake was run with:
>

gcc 9 is not supported with CUDA, as far as I know version 8 is the latest
supported gcc in CUDA 10.2 (officially "native support" whatever they mean
by that is for 7.3 on Ubuntu 18.04.3, see
https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html)

CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ -DGMX_BUILD_OWN_FFTW=ON
> -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug
>

Don't use a Debug build unless you want to debug the GROMACS tools (it's
slow).

Make sure that you cmake configuration does actually use the gcc version
you intend to use. The default invocation as above will pick up the default
compiler toolchain (e.g. /us/bin/gcc in your case, you can verify that by
opening the CMakeCache.txt file or using ccmake) -- and I think the lack of
proper AVX512 support in your default gcc 5 (which you are stil; using) is
the source of the issues you report below.

You can explicitly set the compiler by passing CMAKE_CXX_COMPILER at the
configure step; for details see
http://manual.gromacs.org/current/install-guide/index.html?highlight=cxx%20compiler#typical-installation

Cheers,
--
Szil?rd


> However now I'm getting an error in make
>
> make VERBOSE=1
>
> error:
>
> [ 25%] Building CXX object
>
> src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o
> In file included from
>
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512.h:46:0,
>                  from
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/simd.h:146,
>                  from
>
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/nbnxm_simd.h:40,
>                  from
>
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp:49:
>
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:
> In function ?void gmx::gatherLoadTransposeHsimd(const float*, const float*,
> const int32_t*, gmx::SimdFloat*, gmx::SimdFloat*) [with int align = 2;
> int32_t = int]?:
>
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:422:28:
> error: the last argument must be scale 1, 2, 4, 8
>      tmp1 = _mm512_castpd_ps(
>                             ^
>
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:424:28:
> error: the last argument must be scale 1, 2, 4, 8
>      tmp2 = _mm512_castpd_ps(
>                             ^
> src/gromacs/CMakeFiles/libgromacs.dir/build.make:13881: recipe for target
>
> 'src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o'
> failed
> make[2]: ***
>
> [src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o]
> Error 1
> CMakeFiles/Makefile2:2910: recipe for target
> 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> Makefile:162: recipe for target 'all' failed
> make: *** [all] Error 2
>
> after doing a 1 hour google I found discussions saying that the error
> (Makefile:162: recipe for target 'all' failed) is too vague with no general
> solution. I found fixes for headers and other files for other programs but
> not fixes for this file. The fix linked below is for gromacs-2018 and a
> different file but the general problem seems to suggest it still is a
> gcc/g++ version compatibility error correct? Any suggestions for this
> error?
>
> https://redmine.gromacs.org/issues/2312
>
>
> Thank you so much,
>
> Ryan
>
>  PS Just to document for anyone else going through what I did for
> Gromacs-2020 these were my steps.
>
> sudo apt-get install gcc g++
> cmake ../ -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
>
>  I then received multiple errors complaining about nvcc/C++
> incompatibility. After researching found errors for previous gromacs
> versions suggesting to use gcc-5 (but as you suggested this error has been
> patched).
>
> sudo apt-get install gcc-5 g++-5
> CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
> -DGMX_GPLUSPLUS_PATH=/usr/bin/g++-5 -DCUDA_HOST_COMPILER=gcc-5
> -DCMAKE_CXX_COMPILER=g++-5 -DCMAKE_C_COMPILER=/usr/bin/gcc-5
> -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug
> -D_FORCE_INLINES=OFF
>
> Received different error described in previous email and solved with your
> suggested solution. The key might be to specifically install latest version
> number i.e.
>
> sudo apt-get install gcc-X g++-X (with X being the largest number
> available).
>
>
>
>
> On Wed, Jan 29, 2020 at 2:05 AM Szil?rd P?ll <pall.szilard at gmail.com>
> wrote:
>
> > Hi Ryan,
> >
> > The issue you linked has been worked around in the build system, so my
> > guess is that the issue you are seeing is not related.
> >
> > I would recommend that you update your software stack to the latest
> version
> > (both CUDA 9.1 and gcc 5 are a few years old). On Ubuntu 18.04 you should
> > be able to get gcc 8 through the package manager. Together with
> > upgrading to the latest CUDA might well solve your issues.
> >
> > Let us know if that worked!
> >
> > Cheers,
> > --
> > Szil?rd
> >
> >
> > On Wed, Jan 29, 2020 at 12:14 AM Ryan Woltz <rlwoltz at ucdavis.edu> wrote:
> >
> > > Hello Gromacs experts,
> > >
> > >           First things first, I apologize for any double post but I
> just
> > > joined the community so I'm very new and only found 1-2 posts related
> to
> > my
> > > problem but the solutions did not work. I have been doing MD for about
> > > 6-months using NAMD but want to also try out Gromacs. That being said I
> > am
> > > slightly familiar with CPU modeling programs like Rosetta, but I am
> > totally
> > > lost when it comes to fixing errors using GPU accelerated code for
> CUDA.
> > I
> > > did find that at one point my error was fixed for an earlier version of
> > > Gromacs but Gromacs-2020 may have resurfaced the same error again, here
> > is
> > > what I think my error is:
> > >
> > > https://redmine.gromacs.org/issues/1982
> > >
> > >     I am running Ubuntu 18.04.03 LTS, and gromacs-2020 I did initially
> > have
> > > the gcc/nvcc incompatible but I think installing and using gcc-5/g++-5
> > > version command in cmake has fixed that issue. I have a NVIDIA card
> with
> > > CUDA-9.1 driver when I type nvcc --version.
> > >
> > > my cmake command is as follows:
> > >
> > > CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
> > > -DGMX_GPLUSPLUS_PATH=/usr/bin/g++-5 -DCUDA_HOST_COMPILER=gcc-5
> > > -DCMAKE_CXX_COMPILER=g++-5 -DCMAKE_C_COMPILER=/usr/bin/gcc-5
> > > -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> > > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug (I
> did
> > > try adding -D_FORCE_INLINES= based on the link above in my running
> > command
> > > but it did not work). I did look at the error log but it is way over my
> > > head. I have in addition deleted the CMakeCache.txt file or the
> unpacked
> > > Gromacs and re-unzipped it to restart the cmake process to make sure it
> > was
> > > starting "clean". Is there any additional information I could provide?
> > Does
> > > anyone have a suggestion? Again I'm sorry if this is a duplicate,
> > > everything I found on other sites was way over my head and I generally
> > > understand what is going on but the forums I read on possible solutions
> > > seem way over my head and I'm afraid I will break the driver if I
> attempt
> > > them (which has happened to me already and the computer required a full
> > > reinstall).
> > >
> > > here is last lines from the build:
> > >
> > > -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable
> > > version "1.11.6", minimum required is "1.5")
> > > -- Looking for C++ include pthread.h
> > > -- Looking for C++ include pthread.h - found
> > > -- Atomic operations found
> > > -- Performing Test PTHREAD_SETAFFINITY
> > > -- Performing Test PTHREAD_SETAFFINITY - Success
> > > -- Adding work-around for issue compiling CUDA code with glibc 2.23
> > > string.h
> > > -- Check for working NVCC/C++ compiler combination with nvcc
> > > '/usr/local/cuda/bin/nvcc'
> > > -- Check for working NVCC/C compiler combination - broken
> > > -- /usr/local/cuda/bin/nvcc standard output: ''
> > > -- /usr/local/cuda/bin/nvcc standard error:
> > >  '/home/rlwoltz/protein_modeling/gromacs-2020/build/gcc-5: No such file
> > or
> > > directory
> > > '
> > > CMake Error at cmake/gmxManageNvccConfig.cmake:189 (message):
> > >   CUDA compiler does not seem to be functional.
> > > Call Stack (most recent call first):
> > >   cmake/gmxManageGPU.cmake:207 (include)
> > >   CMakeLists.txt:577 (gmx_gpu_setup)
> > >
> > >
> > > -- Configuring incomplete, errors occurred!
> > > See also
> > >
> > >
> >
> "/home/rlwoltz/protein_modeling/gromacs-2020/build/CMakeFiles/CMakeOutput.log".
> > > See also
> > >
> > >
> >
> "/home/rlwoltz/protein_modeling/gromacs-2020/build/CMakeFiles/CMakeError.log".
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

From pall.szilard at gmail.com  Thu Jan 30 14:50:34 2020
From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=)
Date: Thu, 30 Jan 2020 13:50:34 -0000
Subject: [gmx-users] gromacs-2020 build gcc/nvcc error
In-Reply-To: <CADvvA5Tj5UYYxyiDH0XN2UE12jYBJGpLhbC0GpJVLaBG2cr_kA@mail.gmail.com>
References: <CADvvA5TGm+YnTiRPBi3WNqyKaGwQZdvA2M0Yoep-6tEDdQuQUA@mail.gmail.com>
	<CANnYEw7GOiPgL0F2cBuSpZKPWUZ=McBYL4TVJkNrWOVS613M9g@mail.gmail.com>
	<CADvvA5Tj5UYYxyiDH0XN2UE12jYBJGpLhbC0GpJVLaBG2cr_kA@mail.gmail.com>
Message-ID: <CANnYEw7exAJWpe5J-Jx8AmytJTxgGz3xnM9qXJj_NPodfhEzow@mail.gmail.com>

Dear Ryan,

On Wed, Jan 29, 2020 at 10:35 PM Ryan Woltz <rlwoltz at ucdavis.edu> wrote:

> Dear Szil?rd,
>
>          Thank you for your quick response. You are correct, after
> issuing sudo apt-get install gcc-9 g++-9 CMake was run with:
>

gcc 9 is not supported with CUDA, as far as I know version 8 is the latest
supported gcc in CUDA 10.2 (officially "native support" whatever they mean
by that is for 7.3 on Ubuntu 18.04.3, see
https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html)

CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ -DGMX_BUILD_OWN_FFTW=ON
> -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug
>

Don't use a Debug build unless you want to debug the GROMACS tools (it's
slow).

Make sure that you cmake configuration does actually use the gcc version
you intend to use. The default invocation as above will pick up the default
compiler toolchain (e.g. /us/bin/gcc in your case, you can verify that by
opening the CMakeCache.txt file or using ccmake) -- and I think the lack of
proper AVX512 support in your default gcc 5 (which you are stil; using) is
the source of the issues you report below.

You can explicitly set the compiler by passing CMAKE_CXX_COMPILER at the
configure step; for details see
http://manual.gromacs.org/current/install-guide/index.html?highlight=cxx%20compiler#typical-installation

Cheers,
--
Szil?rd


> However now I'm getting an error in make
>
> make VERBOSE=1
>
> error:
>
> [ 25%] Building CXX object
>
> src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o
> In file included from
>
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512.h:46:0,
>                  from
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/simd.h:146,
>                  from
>
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/nbnxm_simd.h:40,
>                  from
>
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp:49:
>
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:
> In function ?void gmx::gatherLoadTransposeHsimd(const float*, const float*,
> const int32_t*, gmx::SimdFloat*, gmx::SimdFloat*) [with int align = 2;
> int32_t = int]?:
>
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:422:28:
> error: the last argument must be scale 1, 2, 4, 8
>      tmp1 = _mm512_castpd_ps(
>                             ^
>
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:424:28:
> error: the last argument must be scale 1, 2, 4, 8
>      tmp2 = _mm512_castpd_ps(
>                             ^
> src/gromacs/CMakeFiles/libgromacs.dir/build.make:13881: recipe for target
>
> 'src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o'
> failed
> make[2]: ***
>
> [src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o]
> Error 1
> CMakeFiles/Makefile2:2910: recipe for target
> 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> Makefile:162: recipe for target 'all' failed
> make: *** [all] Error 2
>
> after doing a 1 hour google I found discussions saying that the error
> (Makefile:162: recipe for target 'all' failed) is too vague with no general
> solution. I found fixes for headers and other files for other programs but
> not fixes for this file. The fix linked below is for gromacs-2018 and a
> different file but the general problem seems to suggest it still is a
> gcc/g++ version compatibility error correct? Any suggestions for this
> error?
>
> https://redmine.gromacs.org/issues/2312
>
>
> Thank you so much,
>
> Ryan
>
>  PS Just to document for anyone else going through what I did for
> Gromacs-2020 these were my steps.
>
> sudo apt-get install gcc g++
> cmake ../ -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
>
>  I then received multiple errors complaining about nvcc/C++
> incompatibility. After researching found errors for previous gromacs
> versions suggesting to use gcc-5 (but as you suggested this error has been
> patched).
>
> sudo apt-get install gcc-5 g++-5
> CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
> -DGMX_GPLUSPLUS_PATH=/usr/bin/g++-5 -DCUDA_HOST_COMPILER=gcc-5
> -DCMAKE_CXX_COMPILER=g++-5 -DCMAKE_C_COMPILER=/usr/bin/gcc-5
> -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug
> -D_FORCE_INLINES=OFF
>
> Received different error described in previous email and solved with your
> suggested solution. The key might be to specifically install latest version
> number i.e.
>
> sudo apt-get install gcc-X g++-X (with X being the largest number
> available).
>
>
>
>
> On Wed, Jan 29, 2020 at 2:05 AM Szil?rd P?ll <pall.szilard at gmail.com>
> wrote:
>
> > Hi Ryan,
> >
> > The issue you linked has been worked around in the build system, so my
> > guess is that the issue you are seeing is not related.
> >
> > I would recommend that you update your software stack to the latest
> version
> > (both CUDA 9.1 and gcc 5 are a few years old). On Ubuntu 18.04 you should
> > be able to get gcc 8 through the package manager. Together with
> > upgrading to the latest CUDA might well solve your issues.
> >
> > Let us know if that worked!
> >
> > Cheers,
> > --
> > Szil?rd
> >
> >
> > On Wed, Jan 29, 2020 at 12:14 AM Ryan Woltz <rlwoltz at ucdavis.edu> wrote:
> >
> > > Hello Gromacs experts,
> > >
> > >           First things first, I apologize for any double post but I
> just
> > > joined the community so I'm very new and only found 1-2 posts related
> to
> > my
> > > problem but the solutions did not work. I have been doing MD for about
> > > 6-months using NAMD but want to also try out Gromacs. That being said I
> > am
> > > slightly familiar with CPU modeling programs like Rosetta, but I am
> > totally
> > > lost when it comes to fixing errors using GPU accelerated code for
> CUDA.
> > I
> > > did find that at one point my error was fixed for an earlier version of
> > > Gromacs but Gromacs-2020 may have resurfaced the same error again, here
> > is
> > > what I think my error is:
> > >
> > > https://redmine.gromacs.org/issues/1982
> > >
> > >     I am running Ubuntu 18.04.03 LTS, and gromacs-2020 I did initially
> > have
> > > the gcc/nvcc incompatible but I think installing and using gcc-5/g++-5
> > > version command in cmake has fixed that issue. I have a NVIDIA card
> with
> > > CUDA-9.1 driver when I type nvcc --version.
> > >
> > > my cmake command is as follows:
> > >
> > > CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
> > > -DGMX_GPLUSPLUS_PATH=/usr/bin/g++-5 -DCUDA_HOST_COMPILER=gcc-5
> > > -DCMAKE_CXX_COMPILER=g++-5 -DCMAKE_C_COMPILER=/usr/bin/gcc-5
> > > -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> > > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug (I
> did
> > > try adding -D_FORCE_INLINES= based on the link above in my running
> > command
> > > but it did not work). I did look at the error log but it is way over my
> > > head. I have in addition deleted the CMakeCache.txt file or the
> unpacked
> > > Gromacs and re-unzipped it to restart the cmake process to make sure it
> > was
> > > starting "clean". Is there any additional information I could provide?
> > Does
> > > anyone have a suggestion? Again I'm sorry if this is a duplicate,
> > > everything I found on other sites was way over my head and I generally
> > > understand what is going on but the forums I read on possible solutions
> > > seem way over my head and I'm afraid I will break the driver if I
> attempt
> > > them (which has happened to me already and the computer required a full
> > > reinstall).
> > >
> > > here is last lines from the build:
> > >
> > > -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable
> > > version "1.11.6", minimum required is "1.5")
> > > -- Looking for C++ include pthread.h
> > > -- Looking for C++ include pthread.h - found
> > > -- Atomic operations found
> > > -- Performing Test PTHREAD_SETAFFINITY
> > > -- Performing Test PTHREAD_SETAFFINITY - Success
> > > -- Adding work-around for issue compiling CUDA code with glibc 2.23
> > > string.h
> > > -- Check for working NVCC/C++ compiler combination with nvcc
> > > '/usr/local/cuda/bin/nvcc'
> > > -- Check for working NVCC/C compiler combination - broken
> > > -- /usr/local/cuda/bin/nvcc standard output: ''
> > > -- /usr/local/cuda/bin/nvcc standard error:
> > >  '/home/rlwoltz/protein_modeling/gromacs-2020/build/gcc-5: No such file
> > or
> > > directory
> > > '
> > > CMake Error at cmake/gmxManageNvccConfig.cmake:189 (message):
> > >   CUDA compiler does not seem to be functional.
> > > Call Stack (most recent call first):
> > >   cmake/gmxManageGPU.cmake:207 (include)
> > >   CMakeLists.txt:577 (gmx_gpu_setup)
> > >
> > >
> > > -- Configuring incomplete, errors occurred!
> > > See also
> > >
> > >
> >
> "/home/rlwoltz/protein_modeling/gromacs-2020/build/CMakeFiles/CMakeOutput.log".
> > > See also
> > >
> > >
> >
> "/home/rlwoltz/protein_modeling/gromacs-2020/build/CMakeFiles/CMakeError.log".
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

From ric.concu at gmail.com  Thu Jan 30 15:07:44 2020
From: ric.concu at gmail.com (Riccardo Concu)
Date: Thu, 30 Jan 2020 14:07:44 -0000
Subject: [gmx-users] Analysis with .sh file
Message-ID: <98f305c0-5f3a-1861-bc63-326f0c08977d@gmail.com>

Dear all,

I have recently upgrade my Gromacs to the 2019 version from the 5.0.4 
and I found out that now that while I'm trying to use a .sh, as I was 
doing in the version 5.0.4, now I'm receiving back an error since the 
syntax is wrong. I'm wondering if someone could please help me.

Regards,

Riccardo


From johnwhittake at zedat.fu-berlin.de  Thu Jan 30 15:13:26 2020
From: johnwhittake at zedat.fu-berlin.de (John Whittaker)
Date: Thu, 30 Jan 2020 14:13:26 -0000
Subject: [gmx-users] Analysis with .sh file
In-Reply-To: <98f305c0-5f3a-1861-bc63-326f0c08977d@gmail.com>
References: <98f305c0-5f3a-1861-bc63-326f0c08977d@gmail.com>
Message-ID: <45836.160.45.109.123.1580393602.webmail@webmail.zedat.fu-berlin.de>

What is the command that causes the error and is the error due to
incorrect syntax for bash or gromacs? No one will be able to help without
more information.

- John

> Dear all,
>
> I have recently upgrade my Gromacs to the 2019 version from the 5.0.4
> and I found out that now that while I'm trying to use a .sh, as I was
> doing in the version 5.0.4, now I'm receiving back an error since the
> syntax is wrong. I'm wondering if someone could please help me.
>
> Regards,
>
> Riccardo
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
> a mail to gmx-users-request at gromacs.org.
>



From jalemkul at vt.edu  Thu Jan 30 15:14:59 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Thu, 30 Jan 2020 14:14:59 -0000
Subject: [gmx-users] choice of ?Qm Optimized Energy
In-Reply-To: <CACWq+6_sA7er1FtNOSQdW-ue9bgENahdr6MhnC6bY=5EWWbKQQ@mail.gmail.com>
References: <CACWq+6_sA7er1FtNOSQdW-ue9bgENahdr6MhnC6bY=5EWWbKQQ@mail.gmail.com>
Message-ID: <1b3d846b-184b-25b0-f239-675407eac7b9@vt.edu>



On 1/28/20 1:38 AM, Yogesh Sharma wrote:
> thanks for your response Dr. Justin
> these all values are for same ligand submitted under different molid. All
> have net zero charge. only difference is in dQm optimized energy. I dont
> know weather i have to choose one with lowest value or the highest. Please
> check the link attached https://atb.uq.edu.au/molecule.py?molid=364968

I don't have much experience with ATB but it appears that you're simply 
presented with alternate conformers that may be of lower energy. They're 
all very close in value so I don't know how you might use that information.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From jalemkul at vt.edu  Thu Jan 30 15:15:28 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Thu, 30 Jan 2020 14:15:28 -0000
Subject: [gmx-users] Charmm to Gromacs itps
In-Reply-To: <16feb4a73eb.c6617426182519.3166466143215009082@zoho.com>
References: <16fe66a04c4.ad66ab4a133765.8415873409923566678@zoho.com>
	<4f014a17-e2ff-e32a-2228-1e44003ab325@vt.edu>
	<16feb4a73eb.c6617426182519.3166466143215009082@zoho.com>
Message-ID: <e2d438e9-6b4d-362c-3d34-f39bffb156fb@vt.edu>



On 1/28/20 3:35 AM, atb files wrote:
>          
>
>          
>              @Justin: the lipid is not yet added to the charmm directory. Any script?


How did you produce the original PSF?

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From tarzan11_11 at yahoo.com  Thu Jan 30 15:24:05 2020
From: tarzan11_11 at yahoo.com (tarzan p)
Date: Thu, 30 Jan 2020 14:24:05 -0000
Subject: [gmx-users] 3D monitors
References: <2141569556.1500215.1580394239642.ref@mail.yahoo.com>
Message-ID: <2141569556.1500215.1580394239642@mail.yahoo.com>

Hi all..Am looking for some good 3D monitors (either passive or active)Need suggestions for some good 3D monitors for protein structure and interactions visualization...
with best wishes

From sli259 at g.uky.edu  Thu Jan 30 15:58:06 2020
From: sli259 at g.uky.edu (Li, Shi)
Date: Thu, 30 Jan 2020 14:58:06 -0000
Subject: [gmx-users] Analysis with .sh file
In-Reply-To: <mailman.1111.1580393729.1966.gromacs.org_gmx-users@maillist.sys.kth.se>
References: <mailman.1111.1580393729.1966.gromacs.org_gmx-users@maillist.sys.kth.se>
Message-ID: <CAC+hMcAQhU+J0mCudNCiydYM2EnK4_ttx+7EX+v-uFS12KUn=Q@mail.gmail.com>

>
>
> Dear all,
>
> I have recently upgrade my Gromacs to the 2019 version from the 5.0.4
> and I found out that now that while I'm trying to use a .sh, as I was
> doing in the version 5.0.4, now I'm receiving back an error since the
> syntax is wrong. I'm wondering if someone could please help me.
>
>
What is the script in your .sh file? There is not enough information to
find out what goes wrong.



> Regards,
>
> Riccardo
>
>
>
> ------------------------------
>
>

From ashmakhan200 at gmail.com  Thu Jan 30 16:00:09 2020
From: ashmakhan200 at gmail.com (Ashma Khan)
Date: Thu, 30 Jan 2020 15:00:09 -0000
Subject: [gmx-users] Regarding rdf and number of molecules in the FSS of
	tetramer
Message-ID: <CAG89CR68btyevasAkXz+-npAiBCo8fa9k6sm+QRDLF4EafXF4Q@mail.gmail.com>

Dear user's
I have calculated the rdf of urea molecules around the peptides for
different concentration of urea and obtained that peak height of first
solvation shell (FSS) decreases with increase in concentration of urea.
After that I have calculated the number of urea molecules in FSS and found
that urea molecules in the FSS increases with concentration of urea. There
is no correlation between the peak height of FSS and number of urea
molecules. Can anybody suggest me ? what is the reason
The command I have used is
gmx rdf -f md.xtc -s md.tpr -o rdf.xvg -selrpos whole_res_com -seltype
whole_res_com
gmx select -f md.xtc -s md.tpr -os number.xvg -select "resname URE and
within 0.5 of group protein" -selrpos whole_res_com -seltype whole_res_com


-- 
Ashma Khan
Research Scholar
Department of Chemistry
AMU, Aligarh

From yogesh.rma13 at gmail.com  Thu Jan 30 21:02:47 2020
From: yogesh.rma13 at gmail.com (Yogesh Sharma)
Date: Thu, 30 Jan 2020 20:02:47 -0000
Subject: [gmx-users] Customize gromac FF for lipid parameters
Message-ID: <CACWq+6_7TSkH4ajiYLOYOMwGjxBxG6J=wwXbP5y9CBG7cfzP4w@mail.gmail.com>

Hey everyone,
I have a membrane patch generated by charmm gui. I want to customize my
gromac forcefield in accordance with it. I want some suggestion in
extracting information from charmmff. I guess i need information to add in
ffbonded and ffnonbonded files. Can someone help me with it

I don't want to run simulations in charmmff


-- 
 *  with  regards*
*Yogesh Sharma*

From jalemkul at vt.edu  Thu Jan 30 21:27:34 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Thu, 30 Jan 2020 20:27:34 -0000
Subject: [gmx-users] Customize gromac FF for lipid parameters
In-Reply-To: <CACWq+6_7TSkH4ajiYLOYOMwGjxBxG6J=wwXbP5y9CBG7cfzP4w@mail.gmail.com>
References: <CACWq+6_7TSkH4ajiYLOYOMwGjxBxG6J=wwXbP5y9CBG7cfzP4w@mail.gmail.com>
Message-ID: <daad3828-013e-bbbb-6466-1dde6aae583b@vt.edu>



On 1/30/20 3:02 PM, Yogesh Sharma wrote:
> Hey everyone,
> I have a membrane patch generated by charmm gui. I want to customize my
> gromac forcefield in accordance with it. I want some suggestion in
> extracting information from charmmff. I guess i need information to add in
> ffbonded and ffnonbonded files. Can someone help me with it
>
> I don't want to run simulations in charmmff
>

I don't understand what you're trying to do. You want to add parameters 
to the CHARMM force field but you don't want to use CHARMM? If you want 
to use different parameters or a different force field, don't hack an 
existing one. There's no reason to do that.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From rlwoltz at ucdavis.edu  Thu Jan 30 23:30:35 2020
From: rlwoltz at ucdavis.edu (Ryan Woltz)
Date: Thu, 30 Jan 2020 22:30:35 -0000
Subject: [gmx-users] gromacs-2020 build gcc/nvcc error
In-Reply-To: <CANnYEw7exAJWpe5J-Jx8AmytJTxgGz3xnM9qXJj_NPodfhEzow@mail.gmail.com>
References: <CADvvA5TGm+YnTiRPBi3WNqyKaGwQZdvA2M0Yoep-6tEDdQuQUA@mail.gmail.com>
	<CANnYEw7GOiPgL0F2cBuSpZKPWUZ=McBYL4TVJkNrWOVS613M9g@mail.gmail.com>
	<CADvvA5Tj5UYYxyiDH0XN2UE12jYBJGpLhbC0GpJVLaBG2cr_kA@mail.gmail.com>
	<CANnYEw7exAJWpe5J-Jx8AmytJTxgGz3xnM9qXJj_NPodfhEzow@mail.gmail.com>
Message-ID: <CADvvA5QRDqJvTSs71uiZNQf9PX2bZZ87YCU3=t+qLTVp1ampjA@mail.gmail.com>

Dear Szil?rd,

         Thank you so much for your help. I performed the following steps
and it seems to have built successfully, I'll let you know if it does not
run correctly as well.

rm -r gromacs-2020/
sudo apt-get install gcc-8 g++-8
tar -xvzf gromacs-2020.tar.gz
cd gromacs-2020/
mkdir build
cd build
CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ -DGMX_BUILD_OWN_FFTW=ON
-DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=release
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC

Lastly, when I was building in default and ran into trouble I like to build
in debug so it gives details about building and helps me identify source of
the problems or identify relevant information to pass to you so you can
better help me. I appreciate your comment about not building in debugging
mode, but is there a way to run release in verbose mode? When I had
problems with other programs I'd usually build my first time in debugger
mode so I can monitor the process, then make clean and rebuild in default.
Is there a better way to do this?

Once again you help was greatly appreciated,

Ryan

PS again a few notes (if you have time to comment on anything incorrect) I
have for people needing a fix in the future and maybe myself if I do this
again in a few years and forget how.

CUDA version (nvcc --version) is 9.1. This is a little confusing to me
because you referenced CUDA 10.1 and I completely rebuilt this computer in
September 2019, so unless there is a new driver since then it should be
10.1? I grabbed the newest drivers I could find but my computer is
outputting 9.1 so I guess that is my version.

when building gromacs and I specify gcc/g++ verison 5, 8, or 9 it fails
with the original error message regarding glibc 23.2.

CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
-DGMX_GPLUSPLUS_PATH=/usr/bin/g++-8 -DCUDA_HOST_COMPILER=gcc-8
-DCMAKE_CXX_COMPILER=g++-8 -DCMAKE_C_COMPILER=/usr/bin/gcc-8
-DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=release

Do you know why this is? When I started this adventure I just had sudo
apt-get install gcc g++ build-essentials. Then I used gcc-5 g++-5 and
specified the version in the build step, which failed. after taking that
out and running sudo apt-get install gcc-9 g++-9 it passes "CMAKE" but
fails in "make". Based on your suggestions I ran the commands at the top of
the email to which then worked. Would this have worked if I had just
installed gcc-8 g++-8 from the beginning and ran CMAKE with no version
specification?


On Thu, Jan 30, 2020 at 5:50 AM Szil?rd P?ll <pall.szilard at gmail.com> wrote:

> Dear Ryan,
>
> On Wed, Jan 29, 2020 at 10:35 PM Ryan Woltz <rlwoltz at ucdavis.edu> wrote:
>
> > Dear Szil?rd,
> >
> >          Thank you for your quick response. You are correct, after
> > issuing sudo apt-get install gcc-9 g++-9 CMake was run with:
> >
>
> gcc 9 is not supported with CUDA, as far as I know version 8 is the latest
> supported gcc in CUDA 10.2 (officially "native support" whatever they mean
> by that is for 7.3 on Ubuntu 18.04.3, see
> https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html)
>
> CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ -DGMX_BUILD_OWN_FFTW=ON
> > -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug
> >
>
> Don't use a Debug build unless you want to debug the GROMACS tools (it's
> slow).
>
> Make sure that you cmake configuration does actually use the gcc version
> you intend to use. The default invocation as above will pick up the default
> compiler toolchain (e.g. /us/bin/gcc in your case, you can verify that by
> opening the CMakeCache.txt file or using ccmake) -- and I think the lack of
> proper AVX512 support in your default gcc 5 (which you are stil; using) is
> the source of the issues you report below.
>
> You can explicitly set the compiler by passing CMAKE_CXX_COMPILER at the
> configure step; for details see
>
> http://manual.gromacs.org/current/install-guide/index.html?highlight=cxx%20compiler#typical-installation
>
> Cheers,
> --
> Szil?rd
>
>
> > However now I'm getting an error in make
> >
> > make VERBOSE=1
> >
> > error:
> >
> > [ 25%] Building CXX object
> >
> >
> src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o
> > In file included from
> >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512.h:46:0,
> >                  from
> > /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/simd.h:146,
> >                  from
> >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/nbnxm_simd.h:40,
> >                  from
> >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp:49:
> >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:
> > In function ?void gmx::gatherLoadTransposeHsimd(const float*, const
> float*,
> > const int32_t*, gmx::SimdFloat*, gmx::SimdFloat*) [with int align = 2;
> > int32_t = int]?:
> >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:422:28:
> > error: the last argument must be scale 1, 2, 4, 8
> >      tmp1 = _mm512_castpd_ps(
> >                             ^
> >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:424:28:
> > error: the last argument must be scale 1, 2, 4, 8
> >      tmp2 = _mm512_castpd_ps(
> >                             ^
> > src/gromacs/CMakeFiles/libgromacs.dir/build.make:13881: recipe for target
> >
> >
> 'src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o'
> > failed
> > make[2]: ***
> >
> >
> [src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o]
> > Error 1
> > CMakeFiles/Makefile2:2910: recipe for target
> > 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
> > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> > Makefile:162: recipe for target 'all' failed
> > make: *** [all] Error 2
> >
> > after doing a 1 hour google I found discussions saying that the error
> > (Makefile:162: recipe for target 'all' failed) is too vague with no
> general
> > solution. I found fixes for headers and other files for other programs
> but
> > not fixes for this file. The fix linked below is for gromacs-2018 and a
> > different file but the general problem seems to suggest it still is a
> > gcc/g++ version compatibility error correct? Any suggestions for this
> > error?
> >
> > https://redmine.gromacs.org/issues/2312
> >
> >
> > Thank you so much,
> >
> > Ryan
> >
> >  PS Just to document for anyone else going through what I did for
> > Gromacs-2020 these were my steps.
> >
> > sudo apt-get install gcc g++
> > cmake ../ -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> -DGMX_GPU=ON
> >
> >  I then received multiple errors complaining about nvcc/C++
> > incompatibility. After researching found errors for previous gromacs
> > versions suggesting to use gcc-5 (but as you suggested this error has
> been
> > patched).
> >
> > sudo apt-get install gcc-5 g++-5
> > CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
> > -DGMX_GPLUSPLUS_PATH=/usr/bin/g++-5 -DCUDA_HOST_COMPILER=gcc-5
> > -DCMAKE_CXX_COMPILER=g++-5 -DCMAKE_C_COMPILER=/usr/bin/gcc-5
> > -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug
> > -D_FORCE_INLINES=OFF
> >
> > Received different error described in previous email and solved with your
> > suggested solution. The key might be to specifically install latest
> version
> > number i.e.
> >
> > sudo apt-get install gcc-X g++-X (with X being the largest number
> > available).
> >
> >
> >
> >
> > On Wed, Jan 29, 2020 at 2:05 AM Szil?rd P?ll <pall.szilard at gmail.com>
> > wrote:
> >
> > > Hi Ryan,
> > >
> > > The issue you linked has been worked around in the build system, so my
> > > guess is that the issue you are seeing is not related.
> > >
> > > I would recommend that you update your software stack to the latest
> > version
> > > (both CUDA 9.1 and gcc 5 are a few years old). On Ubuntu 18.04 you
> should
> > > be able to get gcc 8 through the package manager. Together with
> > > upgrading to the latest CUDA might well solve your issues.
> > >
> > > Let us know if that worked!
> > >
> > > Cheers,
> > > --
> > > Szil?rd
> > >
> > >
> > > On Wed, Jan 29, 2020 at 12:14 AM Ryan Woltz <rlwoltz at ucdavis.edu>
> wrote:
> > >
> > > > Hello Gromacs experts,
> > > >
> > > >           First things first, I apologize for any double post but I
> > just
> > > > joined the community so I'm very new and only found 1-2 posts related
> > to
> > > my
> > > > problem but the solutions did not work. I have been doing MD for
> about
> > > > 6-months using NAMD but want to also try out Gromacs. That being
> said I
> > > am
> > > > slightly familiar with CPU modeling programs like Rosetta, but I am
> > > totally
> > > > lost when it comes to fixing errors using GPU accelerated code for
> > CUDA.
> > > I
> > > > did find that at one point my error was fixed for an earlier version
> of
> > > > Gromacs but Gromacs-2020 may have resurfaced the same error again,
> here
> > > is
> > > > what I think my error is:
> > > >
> > > > https://redmine.gromacs.org/issues/1982
> > > >
> > > >     I am running Ubuntu 18.04.03 LTS, and gromacs-2020 I did
> initially
> > > have
> > > > the gcc/nvcc incompatible but I think installing and using
> gcc-5/g++-5
> > > > version command in cmake has fixed that issue. I have a NVIDIA card
> > with
> > > > CUDA-9.1 driver when I type nvcc --version.
> > > >
> > > > my cmake command is as follows:
> > > >
> > > > CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
> > > > -DGMX_GPLUSPLUS_PATH=/usr/bin/g++-5 -DCUDA_HOST_COMPILER=gcc-5
> > > > -DCMAKE_CXX_COMPILER=g++-5 -DCMAKE_C_COMPILER=/usr/bin/gcc-5
> > > > -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> > > > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug (I
> > did
> > > > try adding -D_FORCE_INLINES= based on the link above in my running
> > > command
> > > > but it did not work). I did look at the error log but it is way over
> my
> > > > head. I have in addition deleted the CMakeCache.txt file or the
> > unpacked
> > > > Gromacs and re-unzipped it to restart the cmake process to make sure
> it
> > > was
> > > > starting "clean". Is there any additional information I could
> provide?
> > > Does
> > > > anyone have a suggestion? Again I'm sorry if this is a duplicate,
> > > > everything I found on other sites was way over my head and I
> generally
> > > > understand what is going on but the forums I read on possible
> solutions
> > > > seem way over my head and I'm afraid I will break the driver if I
> > attempt
> > > > them (which has happened to me already and the computer required a
> full
> > > > reinstall).
> > > >
> > > > here is last lines from the build:
> > > >
> > > > -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable
> > > > version "1.11.6", minimum required is "1.5")
> > > > -- Looking for C++ include pthread.h
> > > > -- Looking for C++ include pthread.h - found
> > > > -- Atomic operations found
> > > > -- Performing Test PTHREAD_SETAFFINITY
> > > > -- Performing Test PTHREAD_SETAFFINITY - Success
> > > > -- Adding work-around for issue compiling CUDA code with glibc 2.23
> > > > string.h
> > > > -- Check for working NVCC/C++ compiler combination with nvcc
> > > > '/usr/local/cuda/bin/nvcc'
> > > > -- Check for working NVCC/C compiler combination - broken
> > > > -- /usr/local/cuda/bin/nvcc standard output: ''
> > > > -- /usr/local/cuda/bin/nvcc standard error:
> > > >  '/home/rlwoltz/protein_modeling/gromacs-2020/build/gcc-5: No such
> file
> > > or
> > > > directory
> > > > '
> > > > CMake Error at cmake/gmxManageNvccConfig.cmake:189 (message):
> > > >   CUDA compiler does not seem to be functional.
> > > > Call Stack (most recent call first):
> > > >   cmake/gmxManageGPU.cmake:207 (include)
> > > >   CMakeLists.txt:577 (gmx_gpu_setup)
> > > >
> > > >
> > > > -- Configuring incomplete, errors occurred!
> > > > See also
> > > >
> > > >
> > >
> >
> "/home/rlwoltz/protein_modeling/gromacs-2020/build/CMakeFiles/CMakeOutput.log".
> > > > See also
> > > >
> > > >
> > >
> >
> "/home/rlwoltz/protein_modeling/gromacs-2020/build/CMakeFiles/CMakeError.log".
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-request at gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

From rlwoltz at ucdavis.edu  Thu Jan 30 23:30:35 2020
From: rlwoltz at ucdavis.edu (Ryan Woltz)
Date: Thu, 30 Jan 2020 22:30:35 -0000
Subject: [gmx-users] gromacs-2020 build gcc/nvcc error
In-Reply-To: <CANnYEw7exAJWpe5J-Jx8AmytJTxgGz3xnM9qXJj_NPodfhEzow@mail.gmail.com>
References: <CADvvA5TGm+YnTiRPBi3WNqyKaGwQZdvA2M0Yoep-6tEDdQuQUA@mail.gmail.com>
	<CANnYEw7GOiPgL0F2cBuSpZKPWUZ=McBYL4TVJkNrWOVS613M9g@mail.gmail.com>
	<CADvvA5Tj5UYYxyiDH0XN2UE12jYBJGpLhbC0GpJVLaBG2cr_kA@mail.gmail.com>
	<CANnYEw7exAJWpe5J-Jx8AmytJTxgGz3xnM9qXJj_NPodfhEzow@mail.gmail.com>
Message-ID: <CADvvA5QRDqJvTSs71uiZNQf9PX2bZZ87YCU3=t+qLTVp1ampjA@mail.gmail.com>

Dear Szil?rd,

         Thank you so much for your help. I performed the following steps
and it seems to have built successfully, I'll let you know if it does not
run correctly as well.

rm -r gromacs-2020/
sudo apt-get install gcc-8 g++-8
tar -xvzf gromacs-2020.tar.gz
cd gromacs-2020/
mkdir build
cd build
CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ -DGMX_BUILD_OWN_FFTW=ON
-DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=release
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC

Lastly, when I was building in default and ran into trouble I like to build
in debug so it gives details about building and helps me identify source of
the problems or identify relevant information to pass to you so you can
better help me. I appreciate your comment about not building in debugging
mode, but is there a way to run release in verbose mode? When I had
problems with other programs I'd usually build my first time in debugger
mode so I can monitor the process, then make clean and rebuild in default.
Is there a better way to do this?

Once again you help was greatly appreciated,

Ryan

PS again a few notes (if you have time to comment on anything incorrect) I
have for people needing a fix in the future and maybe myself if I do this
again in a few years and forget how.

CUDA version (nvcc --version) is 9.1. This is a little confusing to me
because you referenced CUDA 10.1 and I completely rebuilt this computer in
September 2019, so unless there is a new driver since then it should be
10.1? I grabbed the newest drivers I could find but my computer is
outputting 9.1 so I guess that is my version.

when building gromacs and I specify gcc/g++ verison 5, 8, or 9 it fails
with the original error message regarding glibc 23.2.

CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
-DGMX_GPLUSPLUS_PATH=/usr/bin/g++-8 -DCUDA_HOST_COMPILER=gcc-8
-DCMAKE_CXX_COMPILER=g++-8 -DCMAKE_C_COMPILER=/usr/bin/gcc-8
-DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=release

Do you know why this is? When I started this adventure I just had sudo
apt-get install gcc g++ build-essentials. Then I used gcc-5 g++-5 and
specified the version in the build step, which failed. after taking that
out and running sudo apt-get install gcc-9 g++-9 it passes "CMAKE" but
fails in "make". Based on your suggestions I ran the commands at the top of
the email to which then worked. Would this have worked if I had just
installed gcc-8 g++-8 from the beginning and ran CMAKE with no version
specification?


On Thu, Jan 30, 2020 at 5:50 AM Szil?rd P?ll <pall.szilard at gmail.com> wrote:

> Dear Ryan,
>
> On Wed, Jan 29, 2020 at 10:35 PM Ryan Woltz <rlwoltz at ucdavis.edu> wrote:
>
> > Dear Szil?rd,
> >
> >          Thank you for your quick response. You are correct, after
> > issuing sudo apt-get install gcc-9 g++-9 CMake was run with:
> >
>
> gcc 9 is not supported with CUDA, as far as I know version 8 is the latest
> supported gcc in CUDA 10.2 (officially "native support" whatever they mean
> by that is for 7.3 on Ubuntu 18.04.3, see
> https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html)
>
> CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ -DGMX_BUILD_OWN_FFTW=ON
> > -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug
> >
>
> Don't use a Debug build unless you want to debug the GROMACS tools (it's
> slow).
>
> Make sure that you cmake configuration does actually use the gcc version
> you intend to use. The default invocation as above will pick up the default
> compiler toolchain (e.g. /us/bin/gcc in your case, you can verify that by
> opening the CMakeCache.txt file or using ccmake) -- and I think the lack of
> proper AVX512 support in your default gcc 5 (which you are stil; using) is
> the source of the issues you report below.
>
> You can explicitly set the compiler by passing CMAKE_CXX_COMPILER at the
> configure step; for details see
>
> http://manual.gromacs.org/current/install-guide/index.html?highlight=cxx%20compiler#typical-installation
>
> Cheers,
> --
> Szil?rd
>
>
> > However now I'm getting an error in make
> >
> > make VERBOSE=1
> >
> > error:
> >
> > [ 25%] Building CXX object
> >
> >
> src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o
> > In file included from
> >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512.h:46:0,
> >                  from
> > /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/simd.h:146,
> >                  from
> >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/nbnxm_simd.h:40,
> >                  from
> >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp:49:
> >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:
> > In function ?void gmx::gatherLoadTransposeHsimd(const float*, const
> float*,
> > const int32_t*, gmx::SimdFloat*, gmx::SimdFloat*) [with int align = 2;
> > int32_t = int]?:
> >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:422:28:
> > error: the last argument must be scale 1, 2, 4, 8
> >      tmp1 = _mm512_castpd_ps(
> >                             ^
> >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:424:28:
> > error: the last argument must be scale 1, 2, 4, 8
> >      tmp2 = _mm512_castpd_ps(
> >                             ^
> > src/gromacs/CMakeFiles/libgromacs.dir/build.make:13881: recipe for target
> >
> >
> 'src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o'
> > failed
> > make[2]: ***
> >
> >
> [src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o]
> > Error 1
> > CMakeFiles/Makefile2:2910: recipe for target
> > 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
> > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> > Makefile:162: recipe for target 'all' failed
> > make: *** [all] Error 2
> >
> > after doing a 1 hour google I found discussions saying that the error
> > (Makefile:162: recipe for target 'all' failed) is too vague with no
> general
> > solution. I found fixes for headers and other files for other programs
> but
> > not fixes for this file. The fix linked below is for gromacs-2018 and a
> > different file but the general problem seems to suggest it still is a
> > gcc/g++ version compatibility error correct? Any suggestions for this
> > error?
> >
> > https://redmine.gromacs.org/issues/2312
> >
> >
> > Thank you so much,
> >
> > Ryan
> >
> >  PS Just to document for anyone else going through what I did for
> > Gromacs-2020 these were my steps.
> >
> > sudo apt-get install gcc g++
> > cmake ../ -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> -DGMX_GPU=ON
> >
> >  I then received multiple errors complaining about nvcc/C++
> > incompatibility. After researching found errors for previous gromacs
> > versions suggesting to use gcc-5 (but as you suggested this error has
> been
> > patched).
> >
> > sudo apt-get install gcc-5 g++-5
> > CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
> > -DGMX_GPLUSPLUS_PATH=/usr/bin/g++-5 -DCUDA_HOST_COMPILER=gcc-5
> > -DCMAKE_CXX_COMPILER=g++-5 -DCMAKE_C_COMPILER=/usr/bin/gcc-5
> > -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug
> > -D_FORCE_INLINES=OFF
> >
> > Received different error described in previous email and solved with your
> > suggested solution. The key might be to specifically install latest
> version
> > number i.e.
> >
> > sudo apt-get install gcc-X g++-X (with X being the largest number
> > available).
> >
> >
> >
> >
> > On Wed, Jan 29, 2020 at 2:05 AM Szil?rd P?ll <pall.szilard at gmail.com>
> > wrote:
> >
> > > Hi Ryan,
> > >
> > > The issue you linked has been worked around in the build system, so my
> > > guess is that the issue you are seeing is not related.
> > >
> > > I would recommend that you update your software stack to the latest
> > version
> > > (both CUDA 9.1 and gcc 5 are a few years old). On Ubuntu 18.04 you
> should
> > > be able to get gcc 8 through the package manager. Together with
> > > upgrading to the latest CUDA might well solve your issues.
> > >
> > > Let us know if that worked!
> > >
> > > Cheers,
> > > --
> > > Szil?rd
> > >
> > >
> > > On Wed, Jan 29, 2020 at 12:14 AM Ryan Woltz <rlwoltz at ucdavis.edu>
> wrote:
> > >
> > > > Hello Gromacs experts,
> > > >
> > > >           First things first, I apologize for any double post but I
> > just
> > > > joined the community so I'm very new and only found 1-2 posts related
> > to
> > > my
> > > > problem but the solutions did not work. I have been doing MD for
> about
> > > > 6-months using NAMD but want to also try out Gromacs. That being
> said I
> > > am
> > > > slightly familiar with CPU modeling programs like Rosetta, but I am
> > > totally
> > > > lost when it comes to fixing errors using GPU accelerated code for
> > CUDA.
> > > I
> > > > did find that at one point my error was fixed for an earlier version
> of
> > > > Gromacs but Gromacs-2020 may have resurfaced the same error again,
> here
> > > is
> > > > what I think my error is:
> > > >
> > > > https://redmine.gromacs.org/issues/1982
> > > >
> > > >     I am running Ubuntu 18.04.03 LTS, and gromacs-2020 I did
> initially
> > > have
> > > > the gcc/nvcc incompatible but I think installing and using
> gcc-5/g++-5
> > > > version command in cmake has fixed that issue. I have a NVIDIA card
> > with
> > > > CUDA-9.1 driver when I type nvcc --version.
> > > >
> > > > my cmake command is as follows:
> > > >
> > > > CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
> > > > -DGMX_GPLUSPLUS_PATH=/usr/bin/g++-5 -DCUDA_HOST_COMPILER=gcc-5
> > > > -DCMAKE_CXX_COMPILER=g++-5 -DCMAKE_C_COMPILER=/usr/bin/gcc-5
> > > > -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> > > > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug (I
> > did
> > > > try adding -D_FORCE_INLINES= based on the link above in my running
> > > command
> > > > but it did not work). I did look at the error log but it is way over
> my
> > > > head. I have in addition deleted the CMakeCache.txt file or the
> > unpacked
> > > > Gromacs and re-unzipped it to restart the cmake process to make sure
> it
> > > was
> > > > starting "clean". Is there any additional information I could
> provide?
> > > Does
> > > > anyone have a suggestion? Again I'm sorry if this is a duplicate,
> > > > everything I found on other sites was way over my head and I
> generally
> > > > understand what is going on but the forums I read on possible
> solutions
> > > > seem way over my head and I'm afraid I will break the driver if I
> > attempt
> > > > them (which has happened to me already and the computer required a
> full
> > > > reinstall).
> > > >
> > > > here is last lines from the build:
> > > >
> > > > -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable
> > > > version "1.11.6", minimum required is "1.5")
> > > > -- Looking for C++ include pthread.h
> > > > -- Looking for C++ include pthread.h - found
> > > > -- Atomic operations found
> > > > -- Performing Test PTHREAD_SETAFFINITY
> > > > -- Performing Test PTHREAD_SETAFFINITY - Success
> > > > -- Adding work-around for issue compiling CUDA code with glibc 2.23
> > > > string.h
> > > > -- Check for working NVCC/C++ compiler combination with nvcc
> > > > '/usr/local/cuda/bin/nvcc'
> > > > -- Check for working NVCC/C compiler combination - broken
> > > > -- /usr/local/cuda/bin/nvcc standard output: ''
> > > > -- /usr/local/cuda/bin/nvcc standard error:
> > > >  '/home/rlwoltz/protein_modeling/gromacs-2020/build/gcc-5: No such
> file
> > > or
> > > > directory
> > > > '
> > > > CMake Error at cmake/gmxManageNvccConfig.cmake:189 (message):
> > > >   CUDA compiler does not seem to be functional.
> > > > Call Stack (most recent call first):
> > > >   cmake/gmxManageGPU.cmake:207 (include)
> > > >   CMakeLists.txt:577 (gmx_gpu_setup)
> > > >
> > > >
> > > > -- Configuring incomplete, errors occurred!
> > > > See also
> > > >
> > > >
> > >
> >
> "/home/rlwoltz/protein_modeling/gromacs-2020/build/CMakeFiles/CMakeOutput.log".
> > > > See also
> > > >
> > > >
> > >
> >
> "/home/rlwoltz/protein_modeling/gromacs-2020/build/CMakeFiles/CMakeError.log".
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-request at gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

From miro.astore at gmail.com  Fri Jan 31 02:22:19 2020
From: miro.astore at gmail.com (Miro Astore)
Date: Fri, 31 Jan 2020 01:22:19 -0000
Subject: [gmx-users] constant x-y plane area for membrane simulations.
Message-ID: <CAL3MGYSOzO8GoaLhkbPj2iVFpKo83UyBHdVpWsJ_J7JNdsiMWg@mail.gmail.com>

Hello all,

I'm just wondering if gromacs supports constant x-y plane area for npt
simulations like NAMD does.

Best, Miro

From jalemkul at vt.edu  Fri Jan 31 04:01:13 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Fri, 31 Jan 2020 03:01:13 -0000
Subject: [gmx-users] constant x-y plane area for membrane simulations.
In-Reply-To: <CAL3MGYSOzO8GoaLhkbPj2iVFpKo83UyBHdVpWsJ_J7JNdsiMWg@mail.gmail.com>
References: <CAL3MGYSOzO8GoaLhkbPj2iVFpKo83UyBHdVpWsJ_J7JNdsiMWg@mail.gmail.com>
Message-ID: <e16b0baf-00a7-a733-a58e-8f91c8eb26c3@vt.edu>



On 1/30/20 8:21 PM, Miro Astore wrote:
> Hello all,
>
> I'm just wondering if gromacs supports constant x-y plane area for npt
> simulations like NAMD does.

Use semiisotropic coupling with the x/y compressibility set to zero.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From ric.concu at gmail.com  Fri Jan 31 09:22:21 2020
From: ric.concu at gmail.com (ric.concu at gmail.com)
Date: Fri, 31 Jan 2020 08:22:21 -0000
Subject: [gmx-users] gromacs.org_gmx-users Digest, Vol 189, Issue 80,
	2. Re: Analysis with .sh file (Li, Shi)
Message-ID: <001a01d5d80f$8a5df4a0$9f19dde0$@gmail.com>

Dear all, 

This is an example of a line I have been using on Gromacs 5.0.4:" echo 
    "10" "12" | gmx rdf -f box_tot -s box-npt -n box -o Mol1 &" and this is 
    the error message I'm receiving from Gromacs: "Error in user input:
    Invalid selection '10 12 '
     B  Near '12'
     B B B  syntax error "
Regards,
Riccardo

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
<gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of
gromacs.org_gmx-users-request at maillist.sys.kth.se
Sent: jueves, 30 de enero de 2020 23:31
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: gromacs.org_gmx-users Digest, Vol 189, Issue 80

Send gromacs.org_gmx-users mailing list submissions to
	gromacs.org_gmx-users at maillist.sys.kth.se

To subscribe or unsubscribe via the World Wide Web, visit
	https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
or, via email, send a message with subject or body 'help' to
	gromacs.org_gmx-users-request at maillist.sys.kth.se

You can reach the person managing the list at
	gromacs.org_gmx-users-owner at maillist.sys.kth.se

When replying, please edit your Subject line so it is more specific than
"Re: Contents of gromacs.org_gmx-users digest..."


Today's Topics:

   1. 3D monitors (tarzan p)
   2. Re: Analysis with .sh file (Li, Shi)
   3. Regarding rdf and number of molecules in the FSS of	tetramer
      (Ashma Khan)
   4. Customize gromac FF for lipid parameters (Yogesh Sharma)
   5. Re: Customize gromac FF for lipid parameters (Justin Lemkul)
   6. Re: gromacs-2020 build gcc/nvcc error (Ryan Woltz)


----------------------------------------------------------------------

Message: 1
Date: Thu, 30 Jan 2020 14:23:59 +0000 (UTC)
From: tarzan p <tarzan11_11 at yahoo.com>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Subject: [gmx-users] 3D monitors
Message-ID: <2141569556.1500215.1580394239642 at mail.yahoo.com>
Content-Type: text/plain; charset=UTF-8

Hi all..Am looking for some good 3D monitors (either passive or active)Need
suggestions for some good 3D monitors for protein structure and interactions
visualization...
with best wishes


------------------------------

Message: 2
Date: Thu, 30 Jan 2020 09:50:09 -0500
From: "Li, Shi" <sli259 at g.uky.edu>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] Analysis with .sh file
Message-ID:
	<CAC+hMcAQhU+J0mCudNCiydYM2EnK4_ttx+7EX+v-uFS12KUn=Q at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

>
>
> Dear all,
>
> I have recently upgrade my Gromacs to the 2019 version from the 5.0.4 
> and I found out that now that while I'm trying to use a .sh, as I was 
> doing in the version 5.0.4, now I'm receiving back an error since the 
> syntax is wrong. I'm wondering if someone could please help me.
>
>
What is the script in your .sh file? There is not enough information to find
out what goes wrong.



> Regards,
>
> Riccardo
>
>
>
> ------------------------------
>
>


------------------------------

Message: 3
Date: Thu, 30 Jan 2020 20:29:56 +0530
From: Ashma Khan <ashmakhan200 at gmail.com>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Regarding rdf and number of molecules in the FSS
	of	tetramer
Message-ID:
	<CAG89CR68btyevasAkXz+-npAiBCo8fa9k6sm+QRDLF4EafXF4Q at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

Dear user's
I have calculated the rdf of urea molecules around the peptides for
different concentration of urea and obtained that peak height of first
solvation shell (FSS) decreases with increase in concentration of urea.
After that I have calculated the number of urea molecules in FSS and found
that urea molecules in the FSS increases with concentration of urea. There
is no correlation between the peak height of FSS and number of urea
molecules. Can anybody suggest me ? what is the reason The command I have
used is gmx rdf -f md.xtc -s md.tpr -o rdf.xvg -selrpos whole_res_com
-seltype whole_res_com gmx select -f md.xtc -s md.tpr -os number.xvg -select
"resname URE and within 0.5 of group protein" -selrpos whole_res_com
-seltype whole_res_com


--
Ashma Khan
Research Scholar
Department of Chemistry
AMU, Aligarh


------------------------------

Message: 4
Date: Fri, 31 Jan 2020 01:32:43 +0530
From: Yogesh Sharma <yogesh.rma13 at gmail.com>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Customize gromac FF for lipid parameters
Message-ID:
	<CACWq+6_7TSkH4ajiYLOYOMwGjxBxG6J=wwXbP5y9CBG7cfzP4w at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

Hey everyone,
I have a membrane patch generated by charmm gui. I want to customize my
gromac forcefield in accordance with it. I want some suggestion in
extracting information from charmmff. I guess i need information to add in
ffbonded and ffnonbonded files. Can someone help me with it

I don't want to run simulations in charmmff


-- 
 *  with  regards*
*Yogesh Sharma*


------------------------------

Message: 5
Date: Thu, 30 Jan 2020 15:27:22 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Customize gromac FF for lipid parameters
Message-ID: <daad3828-013e-bbbb-6466-1dde6aae583b at vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 1/30/20 3:02 PM, Yogesh Sharma wrote:
> Hey everyone,
> I have a membrane patch generated by charmm gui. I want to customize my
> gromac forcefield in accordance with it. I want some suggestion in
> extracting information from charmmff. I guess i need information to add in
> ffbonded and ffnonbonded files. Can someone help me with it
>
> I don't want to run simulations in charmmff
>

I don't understand what you're trying to do. You want to add parameters 
to the CHARMM force field but you don't want to use CHARMM? If you want 
to use different parameters or a different force field, don't hack an 
existing one. There's no reason to do that.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================



------------------------------

Message: 6
Date: Thu, 30 Jan 2020 14:30:19 -0800
From: Ryan Woltz <rlwoltz at ucdavis.edu>
To: gmx-users at gromacs.org
Cc: Discussion list for GROMACS users
	<gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: Re: [gmx-users] gromacs-2020 build gcc/nvcc error
Message-ID:
	<CADvvA5QRDqJvTSs71uiZNQf9PX2bZZ87YCU3=t+qLTVp1ampjA at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

Dear Szil?rd,

         Thank you so much for your help. I performed the following steps
and it seems to have built successfully, I'll let you know if it does not
run correctly as well.

rm -r gromacs-2020/
sudo apt-get install gcc-8 g++-8
tar -xvzf gromacs-2020.tar.gz
cd gromacs-2020/
mkdir build
cd build
CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ -DGMX_BUILD_OWN_FFTW=ON
-DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=release
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC

Lastly, when I was building in default and ran into trouble I like to build
in debug so it gives details about building and helps me identify source of
the problems or identify relevant information to pass to you so you can
better help me. I appreciate your comment about not building in debugging
mode, but is there a way to run release in verbose mode? When I had
problems with other programs I'd usually build my first time in debugger
mode so I can monitor the process, then make clean and rebuild in default.
Is there a better way to do this?

Once again you help was greatly appreciated,

Ryan

PS again a few notes (if you have time to comment on anything incorrect) I
have for people needing a fix in the future and maybe myself if I do this
again in a few years and forget how.

CUDA version (nvcc --version) is 9.1. This is a little confusing to me
because you referenced CUDA 10.1 and I completely rebuilt this computer in
September 2019, so unless there is a new driver since then it should be
10.1? I grabbed the newest drivers I could find but my computer is
outputting 9.1 so I guess that is my version.

when building gromacs and I specify gcc/g++ verison 5, 8, or 9 it fails
with the original error message regarding glibc 23.2.

CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
-DGMX_GPLUSPLUS_PATH=/usr/bin/g++-8 -DCUDA_HOST_COMPILER=gcc-8
-DCMAKE_CXX_COMPILER=g++-8 -DCMAKE_C_COMPILER=/usr/bin/gcc-8
-DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=release

Do you know why this is? When I started this adventure I just had sudo
apt-get install gcc g++ build-essentials. Then I used gcc-5 g++-5 and
specified the version in the build step, which failed. after taking that
out and running sudo apt-get install gcc-9 g++-9 it passes "CMAKE" but
fails in "make". Based on your suggestions I ran the commands at the top of
the email to which then worked. Would this have worked if I had just
installed gcc-8 g++-8 from the beginning and ran CMAKE with no version
specification?


On Thu, Jan 30, 2020 at 5:50 AM Szil?rd P?ll <pall.szilard at gmail.com> wrote:

> Dear Ryan,
>
> On Wed, Jan 29, 2020 at 10:35 PM Ryan Woltz <rlwoltz at ucdavis.edu> wrote:
>
> > Dear Szil?rd,
> >
> >          Thank you for your quick response. You are correct, after
> > issuing sudo apt-get install gcc-9 g++-9 CMake was run with:
> >
>
> gcc 9 is not supported with CUDA, as far as I know version 8 is the latest
> supported gcc in CUDA 10.2 (officially "native support" whatever they mean
> by that is for 7.3 on Ubuntu 18.04.3, see
> https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html)
>
> CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ -DGMX_BUILD_OWN_FFTW=ON
> > -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug
> >
>
> Don't use a Debug build unless you want to debug the GROMACS tools (it's
> slow).
>
> Make sure that you cmake configuration does actually use the gcc version
> you intend to use. The default invocation as above will pick up the
default
> compiler toolchain (e.g. /us/bin/gcc in your case, you can verify that by
> opening the CMakeCache.txt file or using ccmake) -- and I think the lack
of
> proper AVX512 support in your default gcc 5 (which you are stil; using) is
> the source of the issues you report below.
>
> You can explicitly set the compiler by passing CMAKE_CXX_COMPILER at the
> configure step; for details see
>
>
http://manual.gromacs.org/current/install-guide/index.html?highlight=cxx%20c
ompiler#typical-installation
>
> Cheers,
> --
> Szil?rd
>
>
> > However now I'm getting an error in make
> >
> > make VERBOSE=1
> >
> > error:
> >
> > [ 25%] Building CXX object
> >
> >
>
src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwT
winCut_VdwLJEwCombGeom_F.cpp.o
> > In file included from
> >
> >
>
/home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_51
2/impl_x86_avx_512.h:46:0,
> >                  from
> > /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/simd.h:146,
> >                  from
> >
> >
>
/home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/nbnxm_simd.h:4
0,
> >                  from
> >
> >
>
/home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/kernels_simd_2
xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp:49:
> >
> >
>
/home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_51
2/impl_x86_avx_512_util_float.h:
> > In function ?void gmx::gatherLoadTransposeHsimd(const float*, const
> float*,
> > const int32_t*, gmx::SimdFloat*, gmx::SimdFloat*) [with int align = 2;
> > int32_t = int]?:
> >
> >
>
/home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_51
2/impl_x86_avx_512_util_float.h:422:28:
> > error: the last argument must be scale 1, 2, 4, 8
> >      tmp1 = _mm512_castpd_ps(
> >                             ^
> >
> >
>
/home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_51
2/impl_x86_avx_512_util_float.h:424:28:
> > error: the last argument must be scale 1, 2, 4, 8
> >      tmp2 = _mm512_castpd_ps(
> >                             ^
> > src/gromacs/CMakeFiles/libgromacs.dir/build.make:13881: recipe for
target
> >
> >
>
'src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw
TwinCut_VdwLJEwCombGeom_F.cpp.o'
> > failed
> > make[2]: ***
> >
> >
>
[src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw
TwinCut_VdwLJEwCombGeom_F.cpp.o]
> > Error 1
> > CMakeFiles/Makefile2:2910: recipe for target
> > 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
> > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> > Makefile:162: recipe for target 'all' failed
> > make: *** [all] Error 2
> >
> > after doing a 1 hour google I found discussions saying that the error
> > (Makefile:162: recipe for target 'all' failed) is too vague with no
> general
> > solution. I found fixes for headers and other files for other programs
> but
> > not fixes for this file. The fix linked below is for gromacs-2018 and a
> > different file but the general problem seems to suggest it still is a
> > gcc/g++ version compatibility error correct? Any suggestions for this
> > error?
> >
> > https://redmine.gromacs.org/issues/2312
> >
> >
> > Thank you so much,
> >
> > Ryan
> >
> >  PS Just to document for anyone else going through what I did for
> > Gromacs-2020 these were my steps.
> >
> > sudo apt-get install gcc g++
> > cmake ../ -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> -DGMX_GPU=ON
> >
> >  I then received multiple errors complaining about nvcc/C++
> > incompatibility. After researching found errors for previous gromacs
> > versions suggesting to use gcc-5 (but as you suggested this error has
> been
> > patched).
> >
> > sudo apt-get install gcc-5 g++-5
> > CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
> > -DGMX_GPLUSPLUS_PATH=/usr/bin/g++-5 -DCUDA_HOST_COMPILER=gcc-5
> > -DCMAKE_CXX_COMPILER=g++-5 -DCMAKE_C_COMPILER=/usr/bin/gcc-5
> > -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug
> > -D_FORCE_INLINES=OFF
> >
> > Received different error described in previous email and solved with
your
> > suggested solution. The key might be to specifically install latest
> version
> > number i.e.
> >
> > sudo apt-get install gcc-X g++-X (with X being the largest number
> > available).
> >
> >
> >
> >
> > On Wed, Jan 29, 2020 at 2:05 AM Szil?rd P?ll <pall.szilard at gmail.com>
> > wrote:
> >
> > > Hi Ryan,
> > >
> > > The issue you linked has been worked around in the build system, so my
> > > guess is that the issue you are seeing is not related.
> > >
> > > I would recommend that you update your software stack to the latest
> > version
> > > (both CUDA 9.1 and gcc 5 are a few years old). On Ubuntu 18.04 you
> should
> > > be able to get gcc 8 through the package manager. Together with
> > > upgrading to the latest CUDA might well solve your issues.
> > >
> > > Let us know if that worked!
> > >
> > > Cheers,
> > > --
> > > Szil?rd
> > >
> > >
> > > On Wed, Jan 29, 2020 at 12:14 AM Ryan Woltz <rlwoltz at ucdavis.edu>
> wrote:
> > >
> > > > Hello Gromacs experts,
> > > >
> > > >           First things first, I apologize for any double post but I
> > just
> > > > joined the community so I'm very new and only found 1-2 posts
related
> > to
> > > my
> > > > problem but the solutions did not work. I have been doing MD for
> about
> > > > 6-months using NAMD but want to also try out Gromacs. That being
> said I
> > > am
> > > > slightly familiar with CPU modeling programs like Rosetta, but I am
> > > totally
> > > > lost when it comes to fixing errors using GPU accelerated code for
> > CUDA.
> > > I
> > > > did find that at one point my error was fixed for an earlier version
> of
> > > > Gromacs but Gromacs-2020 may have resurfaced the same error again,
> here
> > > is
> > > > what I think my error is:
> > > >
> > > > https://redmine.gromacs.org/issues/1982
> > > >
> > > >     I am running Ubuntu 18.04.03 LTS, and gromacs-2020 I did
> initially
> > > have
> > > > the gcc/nvcc incompatible but I think installing and using
> gcc-5/g++-5
> > > > version command in cmake has fixed that issue. I have a NVIDIA card
> > with
> > > > CUDA-9.1 driver when I type nvcc --version.
> > > >
> > > > my cmake command is as follows:
> > > >
> > > > CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
> > > > -DGMX_GPLUSPLUS_PATH=/usr/bin/g++-5 -DCUDA_HOST_COMPILER=gcc-5
> > > > -DCMAKE_CXX_COMPILER=g++-5 -DCMAKE_C_COMPILER=/usr/bin/gcc-5
> > > > -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> > > > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug (I
> > did
> > > > try adding -D_FORCE_INLINES= based on the link above in my running
> > > command
> > > > but it did not work). I did look at the error log but it is way over
> my
> > > > head. I have in addition deleted the CMakeCache.txt file or the
> > unpacked
> > > > Gromacs and re-unzipped it to restart the cmake process to make sure
> it
> > > was
> > > > starting "clean". Is there any additional information I could
> provide?
> > > Does
> > > > anyone have a suggestion? Again I'm sorry if this is a duplicate,
> > > > everything I found on other sites was way over my head and I
> generally
> > > > understand what is going on but the forums I read on possible
> solutions
> > > > seem way over my head and I'm afraid I will break the driver if I
> > attempt
> > > > them (which has happened to me already and the computer required a
> full
> > > > reinstall).
> > > >
> > > > here is last lines from the build:
> > > >
> > > > -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found
suitable
> > > > version "1.11.6", minimum required is "1.5")
> > > > -- Looking for C++ include pthread.h
> > > > -- Looking for C++ include pthread.h - found
> > > > -- Atomic operations found
> > > > -- Performing Test PTHREAD_SETAFFINITY
> > > > -- Performing Test PTHREAD_SETAFFINITY - Success
> > > > -- Adding work-around for issue compiling CUDA code with glibc 2.23
> > > > string.h
> > > > -- Check for working NVCC/C++ compiler combination with nvcc
> > > > '/usr/local/cuda/bin/nvcc'
> > > > -- Check for working NVCC/C compiler combination - broken
> > > > -- /usr/local/cuda/bin/nvcc standard output: ''
> > > > -- /usr/local/cuda/bin/nvcc standard error:
> > > >  '/home/rlwoltz/protein_modeling/gromacs-2020/build/gcc-5: No such
> file
> > > or
> > > > directory
> > > > '
> > > > CMake Error at cmake/gmxManageNvccConfig.cmake:189 (message):
> > > >   CUDA compiler does not seem to be functional.
> > > > Call Stack (most recent call first):
> > > >   cmake/gmxManageGPU.cmake:207 (include)
> > > >   CMakeLists.txt:577 (gmx_gpu_setup)
> > > >
> > > >
> > > > -- Configuring incomplete, errors occurred!
> > > > See also
> > > >
> > > >
> > >
> >
>
"/home/rlwoltz/protein_modeling/gromacs-2020/build/CMakeFiles/CMakeOutput.lo
g".
> > > > See also
> > > >
> > > >
> > >
> >
>
"/home/rlwoltz/protein_modeling/gromacs-2020/build/CMakeFiles/CMakeError.log
".
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-request at gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.


------------------------------

-- 
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-request at gromacs.org.

End of gromacs.org_gmx-users Digest, Vol 189, Issue 80
******************************************************


From duyu at sioc.ac.cn  Fri Jan 31 09:40:49 2020
From: duyu at sioc.ac.cn (Du, Yu)
Date: Fri, 31 Jan 2020 08:40:49 -0000
Subject: [gmx-users] Cell Membrane Potential
In-Reply-To: <CAMC9dP-jycq_Y2g4RTbLZBMh0KErfbba2DAugzsbSLthPZ=cJg@mail.gmail.com>
References: <CAMC9dP-jycq_Y2g4RTbLZBMh0KErfbba2DAugzsbSLthPZ=cJg@mail.gmail.com>
Message-ID: <68f1f10c.b6de.16ffac24ab3.Coremail.duyu@sioc.ac.cn>

Hi Frank, 

I have never conducted any simulation on membrane potential, but you reminded me of the fact that many molecular dynamics simulations on membrane proteins do not consider the membrane potential which is ubiquitous and versatile in biological environment. 

If the membrane potential is a factor in your study, as it's in voltage-gated ion channel system, please refer to previous research papers and the following links:

http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#electric-fields 
http://manual.gromacs.org/documentation/current/reference-manual/special/electric-fields.html


> -----????-----
> ???: "Frank Lam" <franklam66 at gmail.com>
> ????: 2020-01-30 03:55:17 (???)
> ???: gromacs.org_gmx-users at maillist.sys.kth.se
> ??: 
> ??: [gmx-users] Cell Membrane Potential
> 
> Hi,
> 
> I am undergraduate student wanting to learn and use GROMACS for a project
> on membrane proteins. Is altering membrane potential in a simulation
> possible using GROMACS? I do apologize if this is trivial. I tried looking
> at the documentation, but most of the information are currently too
> challenging for me. Any guidance would be greatly appreciated.
> 
> kind regards,
> Frank
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.


--
Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China. 
Zip: 200032, Tel: (86) 021 5492 5275

From atbfiles at zoho.com  Fri Jan 31 14:27:27 2020
From: atbfiles at zoho.com (atb files)
Date: Fri, 31 Jan 2020 13:27:27 -0000
Subject: [gmx-users] Charmm to Gromacs itps
In-Reply-To: <e2d438e9-6b4d-362c-3d34-f39bffb156fb@vt.edu>
References: <16fe66a04c4.ad66ab4a133765.8415873409923566678@zoho.com>
	<4f014a17-e2ff-e32a-2228-1e44003ab325@vt.edu>
	<16feb4a73eb.c6617426182519.3166466143215009082@zoho.com>
	<e2d438e9-6b4d-362c-3d34-f39bffb156fb@vt.edu>
Message-ID: <16ffbc72a17.111f0d4f9117465.6369411725928786093@zoho.com>


        

        
            The files are given on the following server:https://terpconnect.umd.edu/~jbklauda/memb.htmlThey have simulated systems using NAMD.?-Yogesh---- On Thu, 30 Jan 2020 19:45:16 +0530  Justin Lemkul<jalemkul at vt.edu> wrote ----  On 1/28/20 3:35 AM, atb files wrote: >           > >           >              @Justin: the lipid is not yet added to the charmm directory. Any script?   How did you produce the original PSF?  -Justin  --  ==================================================  Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall  Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061  jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com  ==================================================  --  Gromacs Users mailing list  * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!  * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists  * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. 
        
        

    
    


From alessandra.villa.biosim at gmail.com  Fri Jan 31 14:48:40 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Fri, 31 Jan 2020 13:48:40 -0000
Subject: [gmx-users] How to use TIP4P-ICE water model
In-Reply-To: <1eef5fd039bdc2cd0c256d2dc33abcf0@iitk.ac.in>
References: <1eef5fd039bdc2cd0c256d2dc33abcf0@iitk.ac.in>
Message-ID: <CANogp5xx0u2K6xMcce-k0VD6hYAbtwBGUTF++g4NFZaCM86J8A@mail.gmail.com>

Hi,
I did not fully understand what you have done. But my suggestion will be to
use the pre-build tip4p.gro to build the water box and then perform the
simulation with the  topology of tip4p-ice and run long enough to allow the
molecular system to relax, then check RDF. If the profile is not what
expect, cross check the TIP4P-ICE topology file.    Best regards
Alessandra


On Thu, Jan 30, 2020 at 10:26 AM mbhendle <mbhendle at iitk.ac.in> wrote:

> Dear all,
>
> I want to use TIP4P-ICE water model for my simulations, but inbuilt .gro
> file of TIP4P-ICE is not available in Gromacs 2018. I tried alternate
> method by solvating using TIP4P model and then by changing the "itp"
> file of TIP4P in topology file with that of TIP4P-ICE.
>
> But the result of this simulation(RDF) is very different from that of
> literature. Please suggest any alternate approach.
>
> Thanks & Regards,
>
> Mangesh Bhendale
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From alessandra.villa.biosim at gmail.com  Fri Jan 31 14:48:43 2020
From: alessandra.villa.biosim at gmail.com (Alessandra Villa)
Date: Fri, 31 Jan 2020 13:48:43 -0000
Subject: [gmx-users] How to use TIP4P-ICE water model
In-Reply-To: <1eef5fd039bdc2cd0c256d2dc33abcf0@iitk.ac.in>
References: <1eef5fd039bdc2cd0c256d2dc33abcf0@iitk.ac.in>
Message-ID: <CANogp5xx0u2K6xMcce-k0VD6hYAbtwBGUTF++g4NFZaCM86J8A@mail.gmail.com>

Hi,
I did not fully understand what you have done. But my suggestion will be to
use the pre-build tip4p.gro to build the water box and then perform the
simulation with the  topology of tip4p-ice and run long enough to allow the
molecular system to relax, then check RDF. If the profile is not what
expect, cross check the TIP4P-ICE topology file.    Best regards
Alessandra


On Thu, Jan 30, 2020 at 10:26 AM mbhendle <mbhendle at iitk.ac.in> wrote:

> Dear all,
>
> I want to use TIP4P-ICE water model for my simulations, but inbuilt .gro
> file of TIP4P-ICE is not available in Gromacs 2018. I tried alternate
> method by solvating using TIP4P model and then by changing the "itp"
> file of TIP4P in topology file with that of TIP4P-ICE.
>
> But the result of this simulation(RDF) is very different from that of
> literature. Please suggest any alternate approach.
>
> Thanks & Regards,
>
> Mangesh Bhendale
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From jalemkul at vt.edu  Fri Jan 31 14:55:28 2020
From: jalemkul at vt.edu (Justin Lemkul)
Date: Fri, 31 Jan 2020 13:55:28 -0000
Subject: [gmx-users] Charmm to Gromacs itps
In-Reply-To: <16ffbc72a17.111f0d4f9117465.6369411725928786093@zoho.com>
References: <16fe66a04c4.ad66ab4a133765.8415873409923566678@zoho.com>
	<4f014a17-e2ff-e32a-2228-1e44003ab325@vt.edu>
	<16feb4a73eb.c6617426182519.3166466143215009082@zoho.com>
	<e2d438e9-6b4d-362c-3d34-f39bffb156fb@vt.edu>
	<16ffbc72a17.111f0d4f9117465.6369411725928786093@zoho.com>
Message-ID: <e137709a-d6a9-6a46-3666-25e0c56b0b29@vt.edu>



On 1/31/20 8:25 AM, atb files wrote:
>          
>
>          
>              The files are given on the following server:https://terpconnect.umd.edu/~jbklauda/memb.htmlThey have simulated systems using NAMD.

If the individual topologies are not available anywhere, just a PSF, 
then you will have to write your own converter program to transform the 
PSF into GROMACS .top format. PSF is very verbose so this should be 
straightforward.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================


From miro.astore at gmail.com  Fri Jan 31 15:54:51 2020
From: miro.astore at gmail.com (Miro Astore)
Date: Fri, 31 Jan 2020 14:54:51 -0000
Subject: [gmx-users] Charmm to Gromacs itps
In-Reply-To: <e137709a-d6a9-6a46-3666-25e0c56b0b29@vt.edu>
References: <16fe66a04c4.ad66ab4a133765.8415873409923566678@zoho.com>
	<4f014a17-e2ff-e32a-2228-1e44003ab325@vt.edu>
	<16feb4a73eb.c6617426182519.3166466143215009082@zoho.com>
	<e2d438e9-6b4d-362c-3d34-f39bffb156fb@vt.edu>
	<16ffbc72a17.111f0d4f9117465.6369411725928786093@zoho.com>
	<e137709a-d6a9-6a46-3666-25e0c56b0b29@vt.edu>
Message-ID: <CAL3MGYQ7kBD=WudqzOkwhja-OyRWGJOW6C4Oj3K=eiopny=iuA@mail.gmail.com>

Would topotools in vmd not work in this context? I haven't used it but read
about it recently and it would seem this is the use case. Of course you
also need parameters. Wondering.

Best, Miro

Le sam. 1 f?vr. 2020 ? 00:55, Justin Lemkul <jalemkul at vt.edu> a ?crit :

>
>
> On 1/31/20 8:25 AM, atb files wrote:
> >
> >
> >
> >              The files are given on the following server:
> https://terpconnect.umd.edu/~jbklauda/memb.htmlThey have simulated
> systems using NAMD.
>
> If the individual topologies are not available anywhere, just a PSF,
> then you will have to write your own converter program to transform the
> PSF into GROMACS .top format. PSF is very verbose so this should be
> straightforward.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

From pall.szilard at gmail.com  Fri Jan 31 20:01:06 2020
From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=)
Date: Fri, 31 Jan 2020 19:01:06 -0000
Subject: [gmx-users] gromacs-2020 build gcc/nvcc error
In-Reply-To: <CADvvA5QRDqJvTSs71uiZNQf9PX2bZZ87YCU3=t+qLTVp1ampjA@mail.gmail.com>
References: <CADvvA5TGm+YnTiRPBi3WNqyKaGwQZdvA2M0Yoep-6tEDdQuQUA@mail.gmail.com>
	<CANnYEw7GOiPgL0F2cBuSpZKPWUZ=McBYL4TVJkNrWOVS613M9g@mail.gmail.com>
	<CADvvA5Tj5UYYxyiDH0XN2UE12jYBJGpLhbC0GpJVLaBG2cr_kA@mail.gmail.com>
	<CANnYEw7exAJWpe5J-Jx8AmytJTxgGz3xnM9qXJj_NPodfhEzow@mail.gmail.com>
	<CADvvA5QRDqJvTSs71uiZNQf9PX2bZZ87YCU3=t+qLTVp1ampjA@mail.gmail.com>
Message-ID: <CANnYEw5gn=LmBhYU468ien2JPwDVei+28hJPEtrANfpft6HvFA@mail.gmail.com>

Dear Ryan,


On Thu, Jan 30, 2020 at 11:31 PM Ryan Woltz <rlwoltz at ucdavis.edu> wrote:

> Dear Szil?rd,
>
>          Thank you so much for your help. I performed the following steps
> and it seems to have built successfully, I'll let you know if it does not
> run correctly as well.
>
> rm -r gromacs-2020/
> sudo apt-get install gcc-8 g++-8
> tar -xvzf gromacs-2020.tar.gz
> cd gromacs-2020/
> mkdir build
> cd build
> CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ -DGMX_BUILD_OWN_FFTW=ON
> -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=release
>

Note that you are still using the _default_ gcc installation, that is gcc 7
on Ubuntu 18.04. You should see on the first line on the console when you
run cmake something like:
-- The C compiler identification is GNU 7.4.0
-- The CXX compiler identification is GNU 7.4.0
which will clearly indicate the version of the compiler detected.

Unless you tell cmake to use the apt-get installed gcc-8, it will not use
it (and you can also verify that by inspecting the CMAKE_CXX_COMPILER
string in the CMakeCache.txt file).

make
> make check
> sudo make install
> source /usr/local/gromacs/bin/GMXRC
>
> Lastly, when I was building in default and ran into trouble I like to build
> in debug so it gives details about building and helps me identify source of
> the problems or identify relevant information to pass to you so you can
> better help me. I appreciate your comment about not building in debugging
> mode, but is there a way to run release in verbose mode? When I had
> problems with other programs I'd usually build my first time in debugger
> mode so I can monitor the process, then make clean and rebuild in default.
> Is there a better way to do this?
>

A "Debug" build (i.e. when you use CMAKE_BUILD_TYPE=Debug), is useful to
compile a program for running in a debugger (like gdb). You seem to instead
want a way to "debug" build-time issues. A debug build will not help in
that, you will not get additional information about compilation issues. You
can run "make VERBOSE=1" (regadless of the build type) with makefiles
generated by cmake to get a detailed information on the commands executed
during the build, but unless you have a compile- or link-time failure that
you want to track down that sea of output is generally not too useful.

Configure-time errors are stored by cmake in files listed after the usual
"-- Configuring incomplete, errors occurred!" error (files called
CMakeOutput/CMakeError.txt).


> Once again you help was greatly appreciated,
>
> Ryan
>
> PS again a few notes (if you have time to comment on anything incorrect) I
> have for people needing a fix in the future and maybe myself if I do this
> again in a few years and forget how.
>
> CUDA version (nvcc --version) is 9.1. This is a little confusing to me
> because you referenced CUDA 10.1 and I completely rebuilt this computer in
> September 2019, so unless there is a new driver since then it should be
> 10.1? I grabbed the newest drivers I could find but my computer is
> outputting 9.1 so I guess that is my version.
>

CUDA is not (just) the drivers, it is a number of software components that
allow compiling for and runnig computation on the GPU:
- the CUDA toolkit, latest of which is version 10.2 (as you can see here:
https://developer.nvidia.com/cuda-downloads?target_os=Linux), but the
Ubuntu 18.04 repositories seem to only have 9.1
- a display driver, confusingly versioned with numbers like 418.88 or
430.35, the Ubuntu packages are called "nvidia-driver-VERSION"

These two of course have to be compatible, so if you decide to download the
CUDA 10.2 installer from NVIDIA, this will include a compatible driver. Be
careful to completely remove the NVIDIA drivers installed from the Ubuntu
repositories prior to installing sofware with the NVIDIA installer!


when building gromacs and I specify gcc/g++ verison 5, 8, or 9 it fails
> with the original error message regarding glibc 23.2.
>
> CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
> -DGMX_GPLUSPLUS_PATH=/usr/bin/g++-8 -DCUDA_HOST_COMPILER=gcc-8
> -DCMAKE_CXX_COMPILER=g++-8 -DCMAKE_C_COMPILER=/usr/bin/gcc-8
> -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=release
>

Not sure, but if you want to investigate further, I suggest to start with
installing a more recent CUDA toolkit version, 9.1 is  already about two
years old.

Cheers,
--
Szil?rd


> Do you know why this is? When I started this adventure I just had sudo
> apt-get install gcc g++ build-essentials. Then I used gcc-5 g++-5 and
> specified the version in the build step, which failed. after taking that
> out and running sudo apt-get install gcc-9 g++-9 it passes "CMAKE" but
> fails in "make". Based on your suggestions I ran the commands at the top of
> the email to which then worked. Would this have worked if I had just
> installed gcc-8 g++-8 from the beginning and ran CMAKE with no version
> specification?
>
>
> On Thu, Jan 30, 2020 at 5:50 AM Szil?rd P?ll <pall.szilard at gmail.com>
> wrote:
>
> > Dear Ryan,
> >
> > On Wed, Jan 29, 2020 at 10:35 PM Ryan Woltz <rlwoltz at ucdavis.edu> wrote:
> >
> > > Dear Szil?rd,
> > >
> > >          Thank you for your quick response. You are correct, after
> > > issuing sudo apt-get install gcc-9 g++-9 CMake was run with:
> > >
> >
> > gcc 9 is not supported with CUDA, as far as I know version 8 is the
> latest
> > supported gcc in CUDA 10.2 (officially "native support" whatever they
> mean
> > by that is for 7.3 on Ubuntu 18.04.3, see
> > https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html)
> >
> > CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
> -DGMX_BUILD_OWN_FFTW=ON
> > > -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> > > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug
> > >
> >
> > Don't use a Debug build unless you want to debug the GROMACS tools (it's
> > slow).
> >
> > Make sure that you cmake configuration does actually use the gcc version
> > you intend to use. The default invocation as above will pick up the
> default
> > compiler toolchain (e.g. /us/bin/gcc in your case, you can verify that by
> > opening the CMakeCache.txt file or using ccmake) -- and I think the lack
> of
> > proper AVX512 support in your default gcc 5 (which you are stil; using)
> is
> > the source of the issues you report below.
> >
> > You can explicitly set the compiler by passing CMAKE_CXX_COMPILER at the
> > configure step; for details see
> >
> >
> http://manual.gromacs.org/current/install-guide/index.html?highlight=cxx%20compiler#typical-installation
> >
> > Cheers,
> > --
> > Szil?rd
> >
> >
> > > However now I'm getting an error in make
> > >
> > > make VERBOSE=1
> > >
> > > error:
> > >
> > > [ 25%] Building CXX object
> > >
> > >
> >
> src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o
> > > In file included from
> > >
> > >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512.h:46:0,
> > >                  from
> > >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/simd.h:146,
> > >                  from
> > >
> > >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/nbnxm_simd.h:40,
> > >                  from
> > >
> > >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp:49:
> > >
> > >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:
> > > In function ?void gmx::gatherLoadTransposeHsimd(const float*, const
> > float*,
> > > const int32_t*, gmx::SimdFloat*, gmx::SimdFloat*) [with int align = 2;
> > > int32_t = int]?:
> > >
> > >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:422:28:
> > > error: the last argument must be scale 1, 2, 4, 8
> > >      tmp1 = _mm512_castpd_ps(
> > >                             ^
> > >
> > >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:424:28:
> > > error: the last argument must be scale 1, 2, 4, 8
> > >      tmp2 = _mm512_castpd_ps(
> > >                             ^
> > > src/gromacs/CMakeFiles/libgromacs.dir/build.make:13881: recipe for
> target
> > >
> > >
> >
> 'src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o'
> > > failed
> > > make[2]: ***
> > >
> > >
> >
> [src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o]
> > > Error 1
> > > CMakeFiles/Makefile2:2910: recipe for target
> > > 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
> > > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> > > Makefile:162: recipe for target 'all' failed
> > > make: *** [all] Error 2
> > >
> > > after doing a 1 hour google I found discussions saying that the error
> > > (Makefile:162: recipe for target 'all' failed) is too vague with no
> > general
> > > solution. I found fixes for headers and other files for other programs
> > but
> > > not fixes for this file. The fix linked below is for gromacs-2018 and a
> > > different file but the general problem seems to suggest it still is a
> > > gcc/g++ version compatibility error correct? Any suggestions for this
> > > error?
> > >
> > > https://redmine.gromacs.org/issues/2312
> > >
> > >
> > > Thank you so much,
> > >
> > > Ryan
> > >
> > >  PS Just to document for anyone else going through what I did for
> > > Gromacs-2020 these were my steps.
> > >
> > > sudo apt-get install gcc g++
> > > cmake ../ -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> > -DGMX_GPU=ON
> > >
> > >  I then received multiple errors complaining about nvcc/C++
> > > incompatibility. After researching found errors for previous gromacs
> > > versions suggesting to use gcc-5 (but as you suggested this error has
> > been
> > > patched).
> > >
> > > sudo apt-get install gcc-5 g++-5
> > > CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
> > > -DGMX_GPLUSPLUS_PATH=/usr/bin/g++-5 -DCUDA_HOST_COMPILER=gcc-5
> > > -DCMAKE_CXX_COMPILER=g++-5 -DCMAKE_C_COMPILER=/usr/bin/gcc-5
> > > -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> > > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug
> > > -D_FORCE_INLINES=OFF
> > >
> > > Received different error described in previous email and solved with
> your
> > > suggested solution. The key might be to specifically install latest
> > version
> > > number i.e.
> > >
> > > sudo apt-get install gcc-X g++-X (with X being the largest number
> > > available).
> > >
> > >
> > >
> > >
> > > On Wed, Jan 29, 2020 at 2:05 AM Szil?rd P?ll <pall.szilard at gmail.com>
> > > wrote:
> > >
> > > > Hi Ryan,
> > > >
> > > > The issue you linked has been worked around in the build system, so
> my
> > > > guess is that the issue you are seeing is not related.
> > > >
> > > > I would recommend that you update your software stack to the latest
> > > version
> > > > (both CUDA 9.1 and gcc 5 are a few years old). On Ubuntu 18.04 you
> > should
> > > > be able to get gcc 8 through the package manager. Together with
> > > > upgrading to the latest CUDA might well solve your issues.
> > > >
> > > > Let us know if that worked!
> > > >
> > > > Cheers,
> > > > --
> > > > Szil?rd
> > > >
> > > >
> > > > On Wed, Jan 29, 2020 at 12:14 AM Ryan Woltz <rlwoltz at ucdavis.edu>
> > wrote:
> > > >
> > > > > Hello Gromacs experts,
> > > > >
> > > > >           First things first, I apologize for any double post but I
> > > just
> > > > > joined the community so I'm very new and only found 1-2 posts
> related
> > > to
> > > > my
> > > > > problem but the solutions did not work. I have been doing MD for
> > about
> > > > > 6-months using NAMD but want to also try out Gromacs. That being
> > said I
> > > > am
> > > > > slightly familiar with CPU modeling programs like Rosetta, but I am
> > > > totally
> > > > > lost when it comes to fixing errors using GPU accelerated code for
> > > CUDA.
> > > > I
> > > > > did find that at one point my error was fixed for an earlier
> version
> > of
> > > > > Gromacs but Gromacs-2020 may have resurfaced the same error again,
> > here
> > > > is
> > > > > what I think my error is:
> > > > >
> > > > > https://redmine.gromacs.org/issues/1982
> > > > >
> > > > >     I am running Ubuntu 18.04.03 LTS, and gromacs-2020 I did
> > initially
> > > > have
> > > > > the gcc/nvcc incompatible but I think installing and using
> > gcc-5/g++-5
> > > > > version command in cmake has fixed that issue. I have a NVIDIA card
> > > with
> > > > > CUDA-9.1 driver when I type nvcc --version.
> > > > >
> > > > > my cmake command is as follows:
> > > > >
> > > > > CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
> > > > > -DGMX_GPLUSPLUS_PATH=/usr/bin/g++-5 -DCUDA_HOST_COMPILER=gcc-5
> > > > > -DCMAKE_CXX_COMPILER=g++-5 -DCMAKE_C_COMPILER=/usr/bin/gcc-5
> > > > > -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> > > > > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug
> (I
> > > did
> > > > > try adding -D_FORCE_INLINES= based on the link above in my running
> > > > command
> > > > > but it did not work). I did look at the error log but it is way
> over
> > my
> > > > > head. I have in addition deleted the CMakeCache.txt file or the
> > > unpacked
> > > > > Gromacs and re-unzipped it to restart the cmake process to make
> sure
> > it
> > > > was
> > > > > starting "clean". Is there any additional information I could
> > provide?
> > > > Does
> > > > > anyone have a suggestion? Again I'm sorry if this is a duplicate,
> > > > > everything I found on other sites was way over my head and I
> > generally
> > > > > understand what is going on but the forums I read on possible
> > solutions
> > > > > seem way over my head and I'm afraid I will break the driver if I
> > > attempt
> > > > > them (which has happened to me already and the computer required a
> > full
> > > > > reinstall).
> > > > >
> > > > > here is last lines from the build:
> > > > >
> > > > > -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found
> suitable
> > > > > version "1.11.6", minimum required is "1.5")
> > > > > -- Looking for C++ include pthread.h
> > > > > -- Looking for C++ include pthread.h - found
> > > > > -- Atomic operations found
> > > > > -- Performing Test PTHREAD_SETAFFINITY
> > > > > -- Performing Test PTHREAD_SETAFFINITY - Success
> > > > > -- Adding work-around for issue compiling CUDA code with glibc 2.23
> > > > > string.h
> > > > > -- Check for working NVCC/C++ compiler combination with nvcc
> > > > > '/usr/local/cuda/bin/nvcc'
> > > > > -- Check for working NVCC/C compiler combination - broken
> > > > > -- /usr/local/cuda/bin/nvcc standard output: ''
> > > > > -- /usr/local/cuda/bin/nvcc standard error:
> > > > >  '/home/rlwoltz/protein_modeling/gromacs-2020/build/gcc-5: No such
> > file
> > > > or
> > > > > directory
> > > > > '
> > > > > CMake Error at cmake/gmxManageNvccConfig.cmake:189 (message):
> > > > >   CUDA compiler does not seem to be functional.
> > > > > Call Stack (most recent call first):
> > > > >   cmake/gmxManageGPU.cmake:207 (include)
> > > > >   CMakeLists.txt:577 (gmx_gpu_setup)
> > > > >
> > > > >
> > > > > -- Configuring incomplete, errors occurred!
> > > > > See also
> > > > >
> > > > >
> > > >
> > >
> >
> "/home/rlwoltz/protein_modeling/gromacs-2020/build/CMakeFiles/CMakeOutput.log".
> > > > > See also
> > > > >
> > > > >
> > > >
> > >
> >
> "/home/rlwoltz/protein_modeling/gromacs-2020/build/CMakeFiles/CMakeError.log".
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at
> > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > > posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-request at gromacs.org.
> > > > >
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-request at gromacs.org.
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

From pall.szilard at gmail.com  Fri Jan 31 20:01:23 2020
From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=)
Date: Fri, 31 Jan 2020 19:01:23 -0000
Subject: [gmx-users] gromacs-2020 build gcc/nvcc error
In-Reply-To: <CADvvA5QRDqJvTSs71uiZNQf9PX2bZZ87YCU3=t+qLTVp1ampjA@mail.gmail.com>
References: <CADvvA5TGm+YnTiRPBi3WNqyKaGwQZdvA2M0Yoep-6tEDdQuQUA@mail.gmail.com>
	<CANnYEw7GOiPgL0F2cBuSpZKPWUZ=McBYL4TVJkNrWOVS613M9g@mail.gmail.com>
	<CADvvA5Tj5UYYxyiDH0XN2UE12jYBJGpLhbC0GpJVLaBG2cr_kA@mail.gmail.com>
	<CANnYEw7exAJWpe5J-Jx8AmytJTxgGz3xnM9qXJj_NPodfhEzow@mail.gmail.com>
	<CADvvA5QRDqJvTSs71uiZNQf9PX2bZZ87YCU3=t+qLTVp1ampjA@mail.gmail.com>
Message-ID: <CANnYEw5gn=LmBhYU468ien2JPwDVei+28hJPEtrANfpft6HvFA@mail.gmail.com>

Dear Ryan,


On Thu, Jan 30, 2020 at 11:31 PM Ryan Woltz <rlwoltz at ucdavis.edu> wrote:

> Dear Szil?rd,
>
>          Thank you so much for your help. I performed the following steps
> and it seems to have built successfully, I'll let you know if it does not
> run correctly as well.
>
> rm -r gromacs-2020/
> sudo apt-get install gcc-8 g++-8
> tar -xvzf gromacs-2020.tar.gz
> cd gromacs-2020/
> mkdir build
> cd build
> CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ -DGMX_BUILD_OWN_FFTW=ON
> -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=release
>

Note that you are still using the _default_ gcc installation, that is gcc 7
on Ubuntu 18.04. You should see on the first line on the console when you
run cmake something like:
-- The C compiler identification is GNU 7.4.0
-- The CXX compiler identification is GNU 7.4.0
which will clearly indicate the version of the compiler detected.

Unless you tell cmake to use the apt-get installed gcc-8, it will not use
it (and you can also verify that by inspecting the CMAKE_CXX_COMPILER
string in the CMakeCache.txt file).

make
> make check
> sudo make install
> source /usr/local/gromacs/bin/GMXRC
>
> Lastly, when I was building in default and ran into trouble I like to build
> in debug so it gives details about building and helps me identify source of
> the problems or identify relevant information to pass to you so you can
> better help me. I appreciate your comment about not building in debugging
> mode, but is there a way to run release in verbose mode? When I had
> problems with other programs I'd usually build my first time in debugger
> mode so I can monitor the process, then make clean and rebuild in default.
> Is there a better way to do this?
>

A "Debug" build (i.e. when you use CMAKE_BUILD_TYPE=Debug), is useful to
compile a program for running in a debugger (like gdb). You seem to instead
want a way to "debug" build-time issues. A debug build will not help in
that, you will not get additional information about compilation issues. You
can run "make VERBOSE=1" (regadless of the build type) with makefiles
generated by cmake to get a detailed information on the commands executed
during the build, but unless you have a compile- or link-time failure that
you want to track down that sea of output is generally not too useful.

Configure-time errors are stored by cmake in files listed after the usual
"-- Configuring incomplete, errors occurred!" error (files called
CMakeOutput/CMakeError.txt).


> Once again you help was greatly appreciated,
>
> Ryan
>
> PS again a few notes (if you have time to comment on anything incorrect) I
> have for people needing a fix in the future and maybe myself if I do this
> again in a few years and forget how.
>
> CUDA version (nvcc --version) is 9.1. This is a little confusing to me
> because you referenced CUDA 10.1 and I completely rebuilt this computer in
> September 2019, so unless there is a new driver since then it should be
> 10.1? I grabbed the newest drivers I could find but my computer is
> outputting 9.1 so I guess that is my version.
>

CUDA is not (just) the drivers, it is a number of software components that
allow compiling for and runnig computation on the GPU:
- the CUDA toolkit, latest of which is version 10.2 (as you can see here:
https://developer.nvidia.com/cuda-downloads?target_os=Linux), but the
Ubuntu 18.04 repositories seem to only have 9.1
- a display driver, confusingly versioned with numbers like 418.88 or
430.35, the Ubuntu packages are called "nvidia-driver-VERSION"

These two of course have to be compatible, so if you decide to download the
CUDA 10.2 installer from NVIDIA, this will include a compatible driver. Be
careful to completely remove the NVIDIA drivers installed from the Ubuntu
repositories prior to installing sofware with the NVIDIA installer!


when building gromacs and I specify gcc/g++ verison 5, 8, or 9 it fails
> with the original error message regarding glibc 23.2.
>
> CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
> -DGMX_GPLUSPLUS_PATH=/usr/bin/g++-8 -DCUDA_HOST_COMPILER=gcc-8
> -DCMAKE_CXX_COMPILER=g++-8 -DCMAKE_C_COMPILER=/usr/bin/gcc-8
> -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=release
>

Not sure, but if you want to investigate further, I suggest to start with
installing a more recent CUDA toolkit version, 9.1 is  already about two
years old.

Cheers,
--
Szil?rd


> Do you know why this is? When I started this adventure I just had sudo
> apt-get install gcc g++ build-essentials. Then I used gcc-5 g++-5 and
> specified the version in the build step, which failed. after taking that
> out and running sudo apt-get install gcc-9 g++-9 it passes "CMAKE" but
> fails in "make". Based on your suggestions I ran the commands at the top of
> the email to which then worked. Would this have worked if I had just
> installed gcc-8 g++-8 from the beginning and ran CMAKE with no version
> specification?
>
>
> On Thu, Jan 30, 2020 at 5:50 AM Szil?rd P?ll <pall.szilard at gmail.com>
> wrote:
>
> > Dear Ryan,
> >
> > On Wed, Jan 29, 2020 at 10:35 PM Ryan Woltz <rlwoltz at ucdavis.edu> wrote:
> >
> > > Dear Szil?rd,
> > >
> > >          Thank you for your quick response. You are correct, after
> > > issuing sudo apt-get install gcc-9 g++-9 CMake was run with:
> > >
> >
> > gcc 9 is not supported with CUDA, as far as I know version 8 is the
> latest
> > supported gcc in CUDA 10.2 (officially "native support" whatever they
> mean
> > by that is for 7.3 on Ubuntu 18.04.3, see
> > https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html)
> >
> > CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
> -DGMX_BUILD_OWN_FFTW=ON
> > > -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> > > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug
> > >
> >
> > Don't use a Debug build unless you want to debug the GROMACS tools (it's
> > slow).
> >
> > Make sure that you cmake configuration does actually use the gcc version
> > you intend to use. The default invocation as above will pick up the
> default
> > compiler toolchain (e.g. /us/bin/gcc in your case, you can verify that by
> > opening the CMakeCache.txt file or using ccmake) -- and I think the lack
> of
> > proper AVX512 support in your default gcc 5 (which you are stil; using)
> is
> > the source of the issues you report below.
> >
> > You can explicitly set the compiler by passing CMAKE_CXX_COMPILER at the
> > configure step; for details see
> >
> >
> http://manual.gromacs.org/current/install-guide/index.html?highlight=cxx%20compiler#typical-installation
> >
> > Cheers,
> > --
> > Szil?rd
> >
> >
> > > However now I'm getting an error in make
> > >
> > > make VERBOSE=1
> > >
> > > error:
> > >
> > > [ 25%] Building CXX object
> > >
> > >
> >
> src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o
> > > In file included from
> > >
> > >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512.h:46:0,
> > >                  from
> > >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/simd.h:146,
> > >                  from
> > >
> > >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/nbnxm_simd.h:40,
> > >                  from
> > >
> > >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp:49:
> > >
> > >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:
> > > In function ?void gmx::gatherLoadTransposeHsimd(const float*, const
> > float*,
> > > const int32_t*, gmx::SimdFloat*, gmx::SimdFloat*) [with int align = 2;
> > > int32_t = int]?:
> > >
> > >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:422:28:
> > > error: the last argument must be scale 1, 2, 4, 8
> > >      tmp1 = _mm512_castpd_ps(
> > >                             ^
> > >
> > >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:424:28:
> > > error: the last argument must be scale 1, 2, 4, 8
> > >      tmp2 = _mm512_castpd_ps(
> > >                             ^
> > > src/gromacs/CMakeFiles/libgromacs.dir/build.make:13881: recipe for
> target
> > >
> > >
> >
> 'src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o'
> > > failed
> > > make[2]: ***
> > >
> > >
> >
> [src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o]
> > > Error 1
> > > CMakeFiles/Makefile2:2910: recipe for target
> > > 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
> > > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> > > Makefile:162: recipe for target 'all' failed
> > > make: *** [all] Error 2
> > >
> > > after doing a 1 hour google I found discussions saying that the error
> > > (Makefile:162: recipe for target 'all' failed) is too vague with no
> > general
> > > solution. I found fixes for headers and other files for other programs
> > but
> > > not fixes for this file. The fix linked below is for gromacs-2018 and a
> > > different file but the general problem seems to suggest it still is a
> > > gcc/g++ version compatibility error correct? Any suggestions for this
> > > error?
> > >
> > > https://redmine.gromacs.org/issues/2312
> > >
> > >
> > > Thank you so much,
> > >
> > > Ryan
> > >
> > >  PS Just to document for anyone else going through what I did for
> > > Gromacs-2020 these were my steps.
> > >
> > > sudo apt-get install gcc g++
> > > cmake ../ -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> > -DGMX_GPU=ON
> > >
> > >  I then received multiple errors complaining about nvcc/C++
> > > incompatibility. After researching found errors for previous gromacs
> > > versions suggesting to use gcc-5 (but as you suggested this error has
> > been
> > > patched).
> > >
> > > sudo apt-get install gcc-5 g++-5
> > > CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
> > > -DGMX_GPLUSPLUS_PATH=/usr/bin/g++-5 -DCUDA_HOST_COMPILER=gcc-5
> > > -DCMAKE_CXX_COMPILER=g++-5 -DCMAKE_C_COMPILER=/usr/bin/gcc-5
> > > -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> > > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug
> > > -D_FORCE_INLINES=OFF
> > >
> > > Received different error described in previous email and solved with
> your
> > > suggested solution. The key might be to specifically install latest
> > version
> > > number i.e.
> > >
> > > sudo apt-get install gcc-X g++-X (with X being the largest number
> > > available).
> > >
> > >
> > >
> > >
> > > On Wed, Jan 29, 2020 at 2:05 AM Szil?rd P?ll <pall.szilard at gmail.com>
> > > wrote:
> > >
> > > > Hi Ryan,
> > > >
> > > > The issue you linked has been worked around in the build system, so
> my
> > > > guess is that the issue you are seeing is not related.
> > > >
> > > > I would recommend that you update your software stack to the latest
> > > version
> > > > (both CUDA 9.1 and gcc 5 are a few years old). On Ubuntu 18.04 you
> > should
> > > > be able to get gcc 8 through the package manager. Together with
> > > > upgrading to the latest CUDA might well solve your issues.
> > > >
> > > > Let us know if that worked!
> > > >
> > > > Cheers,
> > > > --
> > > > Szil?rd
> > > >
> > > >
> > > > On Wed, Jan 29, 2020 at 12:14 AM Ryan Woltz <rlwoltz at ucdavis.edu>
> > wrote:
> > > >
> > > > > Hello Gromacs experts,
> > > > >
> > > > >           First things first, I apologize for any double post but I
> > > just
> > > > > joined the community so I'm very new and only found 1-2 posts
> related
> > > to
> > > > my
> > > > > problem but the solutions did not work. I have been doing MD for
> > about
> > > > > 6-months using NAMD but want to also try out Gromacs. That being
> > said I
> > > > am
> > > > > slightly familiar with CPU modeling programs like Rosetta, but I am
> > > > totally
> > > > > lost when it comes to fixing errors using GPU accelerated code for
> > > CUDA.
> > > > I
> > > > > did find that at one point my error was fixed for an earlier
> version
> > of
> > > > > Gromacs but Gromacs-2020 may have resurfaced the same error again,
> > here
> > > > is
> > > > > what I think my error is:
> > > > >
> > > > > https://redmine.gromacs.org/issues/1982
> > > > >
> > > > >     I am running Ubuntu 18.04.03 LTS, and gromacs-2020 I did
> > initially
> > > > have
> > > > > the gcc/nvcc incompatible but I think installing and using
> > gcc-5/g++-5
> > > > > version command in cmake has fixed that issue. I have a NVIDIA card
> > > with
> > > > > CUDA-9.1 driver when I type nvcc --version.
> > > > >
> > > > > my cmake command is as follows:
> > > > >
> > > > > CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
> > > > > -DGMX_GPLUSPLUS_PATH=/usr/bin/g++-5 -DCUDA_HOST_COMPILER=gcc-5
> > > > > -DCMAKE_CXX_COMPILER=g++-5 -DCMAKE_C_COMPILER=/usr/bin/gcc-5
> > > > > -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> > > > > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug
> (I
> > > did
> > > > > try adding -D_FORCE_INLINES= based on the link above in my running
> > > > command
> > > > > but it did not work). I did look at the error log but it is way
> over
> > my
> > > > > head. I have in addition deleted the CMakeCache.txt file or the
> > > unpacked
> > > > > Gromacs and re-unzipped it to restart the cmake process to make
> sure
> > it
> > > > was
> > > > > starting "clean". Is there any additional information I could
> > provide?
> > > > Does
> > > > > anyone have a suggestion? Again I'm sorry if this is a duplicate,
> > > > > everything I found on other sites was way over my head and I
> > generally
> > > > > understand what is going on but the forums I read on possible
> > solutions
> > > > > seem way over my head and I'm afraid I will break the driver if I
> > > attempt
> > > > > them (which has happened to me already and the computer required a
> > full
> > > > > reinstall).
> > > > >
> > > > > here is last lines from the build:
> > > > >
> > > > > -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found
> suitable
> > > > > version "1.11.6", minimum required is "1.5")
> > > > > -- Looking for C++ include pthread.h
> > > > > -- Looking for C++ include pthread.h - found
> > > > > -- Atomic operations found
> > > > > -- Performing Test PTHREAD_SETAFFINITY
> > > > > -- Performing Test PTHREAD_SETAFFINITY - Success
> > > > > -- Adding work-around for issue compiling CUDA code with glibc 2.23
> > > > > string.h
> > > > > -- Check for working NVCC/C++ compiler combination with nvcc
> > > > > '/usr/local/cuda/bin/nvcc'
> > > > > -- Check for working NVCC/C compiler combination - broken
> > > > > -- /usr/local/cuda/bin/nvcc standard output: ''
> > > > > -- /usr/local/cuda/bin/nvcc standard error:
> > > > >  '/home/rlwoltz/protein_modeling/gromacs-2020/build/gcc-5: No such
> > file
> > > > or
> > > > > directory
> > > > > '
> > > > > CMake Error at cmake/gmxManageNvccConfig.cmake:189 (message):
> > > > >   CUDA compiler does not seem to be functional.
> > > > > Call Stack (most recent call first):
> > > > >   cmake/gmxManageGPU.cmake:207 (include)
> > > > >   CMakeLists.txt:577 (gmx_gpu_setup)
> > > > >
> > > > >
> > > > > -- Configuring incomplete, errors occurred!
> > > > > See also
> > > > >
> > > > >
> > > >
> > >
> >
> "/home/rlwoltz/protein_modeling/gromacs-2020/build/CMakeFiles/CMakeOutput.log".
> > > > > See also
> > > > >
> > > > >
> > > >
> > >
> >
> "/home/rlwoltz/protein_modeling/gromacs-2020/build/CMakeFiles/CMakeError.log".
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at
> > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > > posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-request at gromacs.org.
> > > > >
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-request at gromacs.org.
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

From hbaumann at uci.edu  Fri Jan 31 20:23:45 2020
From: hbaumann at uci.edu (Hannah Magdalena Baumann)
Date: Fri, 31 Jan 2020 19:23:45 -0000
Subject: [gmx-users] High energies after alignment of trajectory
Message-ID: <6763C446-E901-474B-A19A-7D0222D1B3E2@uci.edu>

Hi,

I want to calculate the free energy difference of turning some position restraints on. Therefore I run two MD simulations, one with the restraints on the protein turned on (I?m restraining the backbone of a specific loop), in the other one I have the restraints turned off. Then I rerun the trajectories of each state with the tpr of the other state and get the free energy difference using BAR. 
But since the protein undergoes rotational and translational movements during the simulations this does not just give me the position restraining energy. So I tried to align the trajectories before the rerun with
gmx trjconv -f prod_md.trr -o pbc.trr -s prod_md.tpr -pbc mol -center
gmx trjconv -f pbc.trr -fit rot+trans -o fit.trr -s prod_md.tpr
But evaluating the energies from this fitted trajectory gives me super large potential energies of the system (~e+12).
Is it generally possible to use a fitted trajectory to evaluate energies? 
Is there something wrong in the way I did the alignment?

Best,
Hannah