[gmx-users] gromacs.org_gmx-users Digest, Vol 131, Issue 130
Mark Abraham
mark.j.abraham at gmail.com
Wed Apr 1 18:42:51 CEST 2015
Hi,
If you're opting for the convenience of recieving the digest, please
consider that replying to it makes it impossible for people to follow the
discussion unless you change the email subject to something useful. In
turn, that might make it slower to get help ;-)
On Wed, Apr 1, 2015 at 6:39 AM, Satyabrata Das <satyabratad04 at gmail.com>
wrote:
> Re: [gmx-users] Installation problem on CRAY XC40----Gromacs-5.0.4
>
> Thank you once again, happy to know that installation is correct.
> Actually during this installation I have not used cc/CC compiler
> wrapper scripts. Presently I am trying to compile with MPI & GPU=on and
> tried to specify compiler wrapper scripts by:
> set CC=cc
> set CXX=CC and then -DCMAKE_C_COMPILER=cc & -DCMAKE_CXX_COMPILER=CC
>
Please give your full command lines. Making us guess wastes everybody's
time :-)
=========
> -- The C compiler identification is GNU 4.8.0
> -- The CXX compiler identification is GNU 4.8.0
> -- Check for working C compiler: /opt/cray/craype/2.2.1/bin/cc
> -- Check for working C compiler: /opt/cray/craype/2.2.1/bin/cc -- works
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- Detecting C compile features
> -- Detecting C compile features - done
> -- Check for working CXX compiler: /opt/cray/craype/2.2.1/bin/CC
> -- Check for working CXX compiler: /opt/cray/craype/2.2.1/bin/CC -- works
>
> Is it correct?
>
> The cmake stage completed successfully. However in 'make' stage showing
> error
> (attached below) and installation stopped. Don't know what to try.
>
CUDA compilation is not working. Does your procedure follow what your site
recommends to do an MPI + GPU compilation? Please read the local
documentation and/or consult with your system admins. The GROMACS build
should just work if you're doing things the way they intend the compiler
toolchains to be used.
Mark
Any hint in this regard will definitely help to progress further.
>
> With best regards,
>
> Satyabrata Das
>
>
> ===============================================================================
> Building NVCC (Device) object
>
> src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/cuda_tools_generated_pmalloc_cuda.cu.o
> Building NVCC (Device) object
>
> src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/gpu_utils_generated_gpu_utils.cu.o
> Building NVCC (Device) object
>
> src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/cuda_tools_generated_copyrite_gpu.cu.o
> Scanning dependencies of target mdrun_objlib
> Building NVCC (Device) object
>
> src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/gpu_utils_generated_memtestG80_core.cu.o
> Scanning dependencies of target view_objlib
> Building NVCC (Device) object
>
> src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/cuda_tools_generated_cudautils.cu.o
> CMake Error at cuda_tools_generated_copyrite_gpu.cu.o.cmake:206 (message):
> Error generating
>
>
> /home/proj/14/physatya/c40/gromacs-5.0.4/build-intel-mkl-mpi/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_copyrite_gpu.cu.o
>
>
> make[2]: ***
>
> [src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/cuda_tools_generated_copyrite_gpu.cu.o]
> Error 1
> make[2]: *** Waiting for unfinished jobs....
> CMake Error at gpu_utils_generated_gpu_utils.cu.o.cmake:206 (message):
> Error generating
>
>
> /home/proj/14/physatya/c40/gromacs-5.0.4/build-intel-mkl-mpi/src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o
>
>
> CMake Error at gpu_utils_generated_memtestG80_core.cu.o.cmake:206
> (message):
> Error generating
>
>
> /home/proj/14/physatya/c40/gromacs-5.0.4/build-intel-mkl-mpi/src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_memtestG80_core.cu.o
>
>
> CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206 (message):
> Error generating
>
>
> /home/proj/14/physatya/c40/gromacs-5.0.4/build-intel-mkl-mpi/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o
>
>
> make[2]: ***
>
> [src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/gpu_utils_generated_gpu_utils.cu.o]
> Error 1
> make[2]: *** Waiting for unfinished jobs....
>
> On Tue, Mar 31, 2015 at 9:08 PM, <
> 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. Re: Setting custom atoms in FF (Justin Lemkul)
> > 2. Re: Advice needed (Justin Lemkul)
> > 3. Re: Advice needed (Priya Das)
> > 4. Re: Installation problem on CRAY XC40----Gromacs-5.0.4
> > (Szil?rd P?ll)
> > 5. Re: Normal mode analysis (Leandro Bortot)
> > 6. Re: [gmx-developers] Problem with creating a topolgy from PDB
> > file (Justin Lemkul)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Tue, 31 Mar 2015 07:40:23 -0400
> > From: Justin Lemkul <jalemkul at vt.edu>
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Subject: Re: [gmx-users] Setting custom atoms in FF
> > Message-ID: <551A87A7.5060104 at vt.edu>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> >
> >
> > On 3/30/15 10:10 PM, Alex wrote:
> > > I am not sure if your answer was a resounding "yes".
> >
> > I don't have the time or desire to build something, test it, and give you
> > an
> > absolute answer :) I can only tell you what the code says, which I can
> do
> > quickly.
> >
> > > I am talking about the label on the left in PDB.
> > >
> >
> > ...which in this case would have to match the entry in the .n2t
> >
> > > Let us say I want to name my atoms "TEST1" and "TEST2" and set up my
> > > PDB as
> > >
> > > ATOM 1 TEST1 CNT A 1 xxx yyy zzz 1.00 0.00
> > > ATOM 2 TEST2 CNT A 1 xxx yyy zzz 1.00 0.00
> > >
> > > and then in atomname2type.a2t I put
> > >
> > > TEST1 opls_996 0 12.011 3 C 0.142 C 0.142 C 0.142
> > > TEST2 opls_1001 0.1 12.011 3 C 0.142 C 0.142 C 0.149
> > >
> > > will the resulting topology contain the distinction despite the issue
> > with bond
> > > lengths? If not, what would be the correct syntax to do that?
> > >
> >
> > This should work (sorry, again I can't be "resounding" in my answer).
> >
> > > I just want to define my atoms in a way that supplements (actually,
> > > precedes) what x2top does when the atoms are not specifically labeled.
> > > A tedious solution in my case, but definitely viable, if this works.
> > >
> >
> > Make a toy system. Three C atoms in a line, the bond length between one
> > of them
> > at 0.149 and the other at 0.142, terminal carbons with different names,
> > and an
> > .n2t entry with two lines, specifying these connections. That will tell
> > you if
> > you're on to something or not.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Tue, 31 Mar 2015 07:42:02 -0400
> > From: Justin Lemkul <jalemkul at vt.edu>
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Advice needed
> > Message-ID: <551A880A.70600 at vt.edu>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> >
> >
> > On 3/31/15 5:25 AM, Priya Das wrote:
> > > Dear all,
> > >
> > > I am working with a transmembrane ion channel and have docked a ligand
> > > which binds to its pore.
> > > The ligand forms only one hydrogen bond with the ion channel.
> > > I want to prove the stability of the binding of this ligand using
> > > protein-ligand dynamics.
> > >
> > > 1) Do i need to convey to the system about the hydrogen bonds , i.e.,
> > > between which atoms are the hydrogen bonds formed ?
> > >
> >
> > Hydrogen bonds arise principally due to electrostatic interactions. You
> > don't
> > provide any sort of information about "this is a hydrogen bond" as part
> of
> > any
> > input.
> >
> > > 2) Is gmx hbonds the command for it?
> > >
> >
> > As the name implies, yes.
> >
> > > 3) In the tutorial (
> > >
> >
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html
> > )
> > > , there is no mention about forming any hydrogen bonds between ligand
> and
> > > protein , then how do we judge that the protein- ligand affinity is
> > stable
> > > in that site or in that conformation?
> > >
> >
> > Hydrogen bonding is one of many possible stabilizing interactions. There
> > is a
> > whole lot more to the story of protein-ligand binding than just hydrogen
> > bonds.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Tue, 31 Mar 2015 17:21:52 +0530
> > From: Priya Das <priyadas001 at gmail.com>
> > To: gmx-users <gmx-users at gromacs.org>
> > Subject: Re: [gmx-users] Advice needed
> > Message-ID:
> > <CAA-mgq5=DjsyF_W2=
> > CEsbPXAFK-xoFPkfsq0yGqQ7w+KiBRGOQ at mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Thankyou Justin.
> >
> > On Tue, Mar 31, 2015 at 5:12 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> > >
> > >
> > > On 3/31/15 5:25 AM, Priya Das wrote:
> > >
> > >> Dear all,
> > >>
> > >> I am working with a transmembrane ion channel and have docked a ligand
> > >> which binds to its pore.
> > >> The ligand forms only one hydrogen bond with the ion channel.
> > >> I want to prove the stability of the binding of this ligand using
> > >> protein-ligand dynamics.
> > >>
> > >> 1) Do i need to convey to the system about the hydrogen bonds , i.e.,
> > >> between which atoms are the hydrogen bonds formed ?
> > >>
> > >>
> > > Hydrogen bonds arise principally due to electrostatic interactions.
> You
> > > don't provide any sort of information about "this is a hydrogen bond"
> as
> > > part of any input.
> > >
> > > 2) Is gmx hbonds the command for it?
> > >>
> > >>
> > > As the name implies, yes.
> > >
> > > 3) In the tutorial (
> > >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> > >> gmx-tutorials/complex/01_pdb2gmx.html)
> > >> , there is no mention about forming any hydrogen bonds between ligand
> > and
> > >> protein , then how do we judge that the protein- ligand affinity is
> > stable
> > >> in that site or in that conformation?
> > >>
> > >>
> > > Hydrogen bonding is one of many possible stabilizing interactions.
> There
> > > is a whole lot more to the story of protein-ligand binding than just
> > > hydrogen bonds.
> > >
> > > -Justin
> > >
> > > --
> > > ==================================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 629
> > > University of Maryland, Baltimore
> > > 20 Penn St.
> > > Baltimore, MD 21201
> > >
> > > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > > http://mackerell.umaryland.edu/~jalemkul
> > >
> > > ==================================================
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> >
> >
> >
> > --
> > *Let us all join hands to save our " Mother Earth"*
> > ------------------------------------------------------------------------
> > Regards,
> > Priya Das
> > Research Scholar
> > Dept. of Computational Biology and Bioinformatics,
> > University of Kerala
> >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Tue, 31 Mar 2015 14:11:36 +0200
> > From: Szil?rd P?ll <pall.szilard at gmail.com>
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Subject: Re: [gmx-users] Installation problem on CRAY
> > XC40----Gromacs-5.0.4
> > Message-ID:
> > <
> > CANnYEw49EXaCJHCyTbmcX7xG7jMXSb+PyYTbA1b7yNOf3kJarQ at mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Nothing unexpected, you can't run on the login node binaries that you
> > compiled for the compute nodes.
> > --
> > Szil?rd
> >
> >
> > On Tue, Mar 31, 2015 at 7:48 AM, Satyabrata Das <satyabratad04 at gmail.com
> >
> > wrote:
> > > Thank you, I will read Cray docs again, presently trying to install
> with
> > > gcc 4.8 because
> > > 4.9 is showing incompatibility error with the available cudatoolkit. It
> > > seems CPU-only
> > > installation is successful. However both built in test case and
> > > regression-test failed with the
> > > following error:
> > >
> > > [Tue Mar 31 00:44:27 2015] [c1-0c0s1n1] Fatal error in MPI_Init: Other
> > MPI
> > > error, error stack:
> > > MPIR_Init_thread(506):
> > > MPID_Init(192).......: channel initialization failed
> > > MPID_Init(569).......: PMI2 init failed: 1
> > >
> > > Kindly help,
> > >
> > > With best regards,
> > >
> > > Satyabrata Das
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Tue, 31 Mar 2015 12:31:13 -0300
> > From: Leandro Bortot <leandro.obt at gmail.com>
> > To: gmx-users <gmx-users at gromacs.org>
> > Subject: Re: [gmx-users] Normal mode analysis
> > Message-ID:
> > <
> > CAGpu61iAUtKvGLbUSqQ-tYcmNUBu+qPuZVs2G2i2iBp8X2V9yg at mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Hi Rahul,
> >
> > Did you make the vacuum minimization with a double-precision version
> > of gromacs using the L-BFGS algorithm? From the protocol you described it
> > seems you didn't do it..
> > What was the maximum force after the minimization? (check the .log
> > file)
> >
> > I hope it helps,
> > Leandro.
> >
> >
> >
> > On Sat, Mar 28, 2015 at 7:26 AM, rahul dhakne <rahuldhakne89 at gmail.com>
> > wrote:
> >
> > > Dear all Gromacs user,
> > >
> > > I am trying to perform the Normal Mode Analysis protein-DNA complex
> > > in vacuum. As the complex is highly negative charge (-163)I performed
> > > the energy minimization of complex in water (to neutralize the
> > > complex). After I get the completely minimized complex, again I have
> > > done energy minimization of complex (in vacuum) for just one step to
> > > get the .trr input file for the Normal mode analysis. As I have to
> > > perform the normal mode analysis in vacuum I did that. But due to
> > > highly negative charge it got stuck in hessian matrix calculation.
> > > Even though it calculate the matrix I got negative eigenvalues after
> > > diagonalizing the matrix.
> > >
> > > I also tried with complete energy minimization in vacuum and proceed
> > > for normal mode calculation, but again stuck with the same problem
> > > i.e. high negative charge (-163)
> > >
> > > How can I neutralize the system??
> > >
> > > or there is any way to do that or probably I am doing something
> unusual??
> > >
> > >
> > > Any suggestions will be very welcomed.
> > >
> > > Thanking you in advance!
> > >
> > > -
> > > Rahul
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> >
> >
> > ------------------------------
> >
> > Message: 6
> > Date: Tue, 31 Mar 2015 11:38:25 -0400
> > From: Justin Lemkul <jalemkul at vt.edu>
> > To: gmx-developers at gromacs.org
> > Cc: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Subject: Re: [gmx-users] [gmx-developers] Problem with creating a
> > topolgy from PDB file
> > Message-ID: <551ABF71.7000506 at vt.edu>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> >
> > Please do not post usage questions on the developers' list. I am CC'ing
> > this
> > over to gmx-users; please continue any discussion there.
> >
> > On 3/31/15 11:36 AM, Asmaa El khodary wrote:
> > > Hi,
> > > I'm a new user of gromacs and I follow some tutorials to run a
> > simulation of
> > > lysozyme using OPLS-AA/L force field . The problem is: when I type the
> > command
> > > *pdb2gmx -f 1LYD.pdb -water tip3p *in the terminal and choose the force
> > field ,I
> > > get this error
> > >
> > > Program pdb2gmx, VERSION 5.0.4
> > > Source code file:
> > > /home/asmaa/Downloads/gromacs-5.0.4/src/gromacs/fileio/futil.cpp, line:
> > 545
> > >
> > > File input/output error:
> > > 1LYD.pdb
> >
> > An I/O error means the file isn't in your working directory (or, less
> > likely,
> > the file isn't readable to you). List your files to verify.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> >
> >
> > ------------------------------
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe 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 131, Issue 130
> > *******************************************************
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
More information about the gromacs.org_gmx-users
mailing list