[gmx-users] gromacs.org_gmx-users Digest, Vol 119, Issue 10

Tom dnaafm at gmail.com
Tue Mar 4 05:03:07 CET 2014


Thanks Justin!
The result about the improper dihedral angle from ParamChem does keep
me very confused. For the molecule (C6H5-NH2), the one of N H H C should
not have improper dihedral however the websever showes there is one.

If anyone has the experience of Charmm improper dihedral, please give a
help. Thanks!

Thom


On Mon, Mar 3, 2014 at 9:57 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. Re: Regarding structure analysis of DNA (Justin Lemkul)
>    2. Re: Set the environment variables of "FFTW3_INCLUDE_DIR" and
>       "FFTW3_LIBRARIES" (Justin Lemkul)
>    3. Re: Two-body Bonded Distance (jolayfield)
>    4. Re: Question about Improper Dihedral of Charmm in gmx &
>       ParamChem (Justin Lemkul)
>    5. md_pull code in umbrella sampling (Arunima Shilpi)
>    6. No default U-B types charmm (gromacs query)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 03 Mar 2014 09:14:51 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Regarding structure analysis of DNA
> Message-ID: <53148E5B.8010402 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 3/3/14, 4:05 AM, Sathish Kumar wrote:
> > Hai
> >            I have done simulation of DNA on carbon nano tube surface. I
> want
> > to calculate structural changes (means changes in stacking, puckering
> > angles and bending of helix) in DNA. Can any suggest me how to calculate
> > these things.
> >
>
> Chapter 8 describes all available analysis tools.  For more complicated
> things,
> you may need outside software like MDAnalysis or similar packages.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> 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: Mon, 03 Mar 2014 09:16:53 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Set the environment variables of
>         "FFTW3_INCLUDE_DIR" and "FFTW3_LIBRARIES"
> Message-ID: <53148ED5.2050804 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 3/3/14, 5:26 AM, Hassan Aaryapour wrote:
> > Dear Gmx-user;
> > I want to install double precision gromacs 4.5.3 and FFTW 3.3.2 in my
> > home directory.
> > first, according to the FFTW installation instructions I installed and
> > introduced it to bash shell it as the following order:
> >
> > $tar -xzvf fftw-3.3.2.tar.gz
> > $./configure --enable-threads --prefix=/home/WeNMR/ProgramFiles/fftw
> > $make
> > $make install
> >
> > export CPPFLAGS=-I/home/WeNMR/ProgramFiles/fftw/include
> > export LDFLAGS=-L/home/WeNMR/ProgramFiles/fftw/lib
> >
> > but it isn't found automatically by cmake when I want to install gromacs.
> > and this error was appeared:
> >
> >   CMake Error at
> >
> /usr/local/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:108
> > (message):
> >     Could not find FFTW3.  Provide the fftw3 install directory in the
> >     FFTW3_ROOT_DIR environment variable.  (missing: FFTW3_LIBRARIES
> >     FFTW3_INCLUDE_DIR)
> >   Call Stack (most recent call first):
> >
> /usr/local/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:315
> > (_FPHSA_FAILURE_MESSAGE)
> >     cmake/FindFFTW3.cmake:31 (find_package_handle_standard_args)
> >     CMakeLists.txt:636 (find_package)
> >
> >
> > How can I set the environment variables for "FFTW3_INCLUDE_DIR" and
> > "FFTW3_LIBRARIES"?
>
> Those are CMake command-line options.  See the full installation
> instructions
> online, specifically
>
> http://www.gromacs.org/Documentation/Installation_Instructions#4.4._Helping_CMake_find_the_right_libraries.2fheaders.2fprograms
>
> Is there any reason you are installing outdated versions of Gromacs and
> FFTW?
>
> -Justin
>
> > can I add my FFTW installed path to "CMakeLists.txt" file in the
> > related section in below? how?
> >
> > if(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
> > #    MESSAGE(STATUS "Using external FFT library - fftw3")
> >      if(GMX_DOUBLE)
> >          find_package(FFTW3 REQUIRED)
> >               include_directories(${FFTW3_INCLUDE_DIR})
> >          set(FFT_LIBRARIES ${FFTW3_LIBRARIES})
> >          set(PKG_FFT "fftw3")
> >      else(GMX_DOUBLE)
> >          find_package(FFTW3F REQUIRED)
> >          include_directories(${FFTW3F_INCLUDE_DIR})
> >          set(FFT_LIBRARIES ${FFTW3F_LIBRARIES})
> >          set(PKG_FFT "fftw3f")
> >      endif(GMX_DOUBLE)
> >
> >
> > Thank you in advance
> > Hassan
> >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> 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: Mon, 3 Mar 2014 06:26:44 -0800 (PST)
> From: jolayfield <jolayfield at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Two-body Bonded Distance
> Message-ID: <1393856804341-5014891.post at n6.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
> Justin,
>
>    The two-body distance is about 4x the actual distance in the structure
> file.  This spuriously large distance only appears once I add the virtual
> particle.  This appears to not affect the actual MD run based on my tests
> with and without the virtual particle, but it does limit the number of
> processors that I am able to use during the run.  Is there a reason that
> the
> distance should be different for the two-body bonded and multi-body bonded
> distance when they span the same atoms?
>
> Thanks,
>
> Josh
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Two-body-Bonded-Distance-tp5014864p5014891.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 03 Mar 2014 09:27:21 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Question about Improper Dihedral of Charmm in
>         gmx & ParamChem
> Message-ID: <53149149.6080902 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 3/3/14, 12:27 AM, Tom wrote:
> > Dear Gromacs Users,
> >
> > I am confused about the definition of improper dihedral angle of Charmm
> > used in gromacs.
> >
> > I used two molecle
> > 1)M1:  C6H5-NH2
> > 2)MP1:  C6H5-NH-C=O
> >                                 |
> >                                CH3
> > After I submitted to the webserver of ParamChem, the output str files in
> > the attachment show that
> >
> > *For M1*, IMPROPERS
> >
> > NG2S3  HGP4   HGP4   CG2R61    -2.5000  0     0.00 ! -2.0 PYRIDINE
> > aminopyridine 11/10 kevo: sic! Compensates for in-plane force from
> > CG2R61 CG2R61 NG2S3 HGP4
> >
> > *For MP1*, IMPROPERS
> > CG2O1 CG331 NG2S1 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK)
> > WILDCARD
> >
> > For M1, with a NH2 group, ParamChem gives an improper dihedral *with N
> as a
> > central atom*.
> >
> > However, for MP1, with a NH1 internal group, ParamChem does not give any
> > dihedrals *with N as a central atom*.
> >
>
> It shouldn't.  The CHARMM force field uses few improper dihedrals in
> general,
> and there are none around N in acetamides.  See examples in model
> compounds like
> NMA, DMA, etc in the CHARMM force fields.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 3 Mar 2014 20:04:09 +0530
> From: Arunima Shilpi <writetoash28 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] md_pull code in umbrella sampling
> Message-ID:
>         <
> CAM90emYcoyZVjVW4Z7xuagSxwKL1y0Y26Bn4EXAxgmZv_hSArw at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear Sir
>
> I am trying to calculate the potential mean force (PMF) between protein
> and Ligand. I have applied position restrain to protein. I have applied
> reference pulling group to Protein and Pulling force has been applied to
> ligand. The pul force is applied along Z-axis. I had query as to whether I
> am proceeding in the right direction. Here I have provided the detail of
> the content of md_pull.mdp
>
> md_pull.mdp
>
> title       = Umbrella pulling simulation
> define      = -DPOSRES_Protein
> ; Run parameters
> integrator  = md
> dt          = 0.002
> tinit       = 0
> nsteps      = 250000    ; 500 ps
> nstcomm     = 10
> ; Output parameters
> nstxout     = 5000      ; every 10 ps
> nstvout     = 5000
> nstfout     = 500
> nstxtcout   = 500       ; every 1 ps
> nstenergy   = 500
> ; Bond parameters
> constraint_algorithm    = lincs
> constraints             = all-bonds
> continuation            = yes       ; continuing from NPT
> ; Single-range cutoff scheme
> nstlist     = 5
> ns_type     = grid
> rlist       = 1.4
> rcoulomb    = 1.4
> rvdw        = 1.4
> ; PME electrostatics parameters
> coulombtype     = PME
> fourierspacing  = 0.12
> fourier_nx      = 0
> fourier_ny      = 0
> fourier_nz      = 0
> pme_order       = 4
> ewald_rtol      = 1e-5
> optimize_fft    = yes
> ; Berendsen temperature coupling is on in two groups
> Tcoupl      = Nose-Hoover
> tc_grps     = Protein   Non-Protein
> tau_t       = 0.5       0.5
> ref_t       = 310       310
> ; Pressure coupling is on
> Pcoupl          = Parrinello-Rahman
> pcoupltype      = isotropic
> tau_p           = 1.0
> compressibility = 4.5e-5
> ref_p           = 1.0
> refcoord_scaling = com
> ; Generate velocities is off
> gen_vel     = no
> ; Periodic boundary conditions are on in all directions
> pbc     = xyz
> ; Long-range dispersion correction
> DispCorr    = EnerPres
> ; Pull code
> pull            = umbrella
> pull_geometry   = distance  ; simple distance increase
> pull_dim        = N N Y
> pull_start      = yes       ; define initial COM distance > 0
> pull_ngroups    = 1
> pull_group0     = Protein
> pull_group1     = DRG
> pull_rate1      = 0.01      ; 0.01 nm per ps = 10 nm per ns
> pull_k1         = 1000      ; kJ mol^-1 nm^-2
>
> Regards
>
>
> Arunima
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 3 Mar 2014 15:57:55 +0000
> From: gromacs query <gromacsquery at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: [gmx-users] No default U-B types charmm
> Message-ID:
>         <
> CAPe3FJAqEu8vb9YMmhin3srwZDAQTbqbatESmwqRcxwG9FGTjg at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi All
>
> I am trying to use charmm36 (charmm36-jan2014 from charmm website) with
> popc membrane built using charmm-gui (have water and ions).
>
> I used commands as follows:
>
> pdb2gmx -f step5_assembly.pdb -o popc.gro -water tip3p -ff charmm36-jan2014
> editconf -f popc.gro -o popc_box.gro -c -d 0.0
> grompp -f minim.mdp -c popc_box.gro -p topol.top -o em.tpr
>
> I get this error: (so many)
> ERROR 11520 [file topol.top, line 184419]:
>   No default U-B types
>
> Where are UB for charmm36?
>
> thanks,
> JIom
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe 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 119, Issue 10
> ******************************************************
>


More information about the gromacs.org_gmx-users mailing list