Re: [gmx-users] nano dimensions

Thank you for the reply. How to carry out simulations of a molecule in nano scale? Thanks, Vidya.R On Fri, Dec 21, 2018 at 7:11 PM Justin Lemkul wrote: > On Fri, Dec 21, 2018 at 6:35 AM Vidya R wrote: > > > Hi gromacs users, > > > > How to specify nano dimension

[gmx-users] nano dimensions

Hi gromacs users, How to specify nano dimensions of an organic compound in the input files of gromacs? Thanks, Vidya.R -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] generating movie file

voice as narration to my glorious trajectory, but was > disappointed. Very useful for supplemental files for journals with IF>10. > Maybe gmx developers should look into that. > > > > On 1/26/2018 9:51 PM, Vidya R wrote: > >> Hi gromacs users, >> >> &g

[gmx-users] generating movie file

Hi gromacs users, Can we generate .mp4 file instead of .pdb using gmx trjconv? Thanks, Vidya.R -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] regarding pbc issue

-center -s PRD.tpr -f trajcluster.xtc -o newtraj.xtc and created a .pdb file with newtraj.xtc, the whole molecule was intact. Thanks, Vidya.R On Sat, Jan 13, 2018 at 7:25 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/13/18 7:53 AM, Vidya R wrote: > >> Hi

[gmx-users] regarding pbc issue

Hi gmx users, I used the following commands after simulation run (organic compound in water, to calculate rdf) gmx trjconv -pbc whole -s PRD.tpr -f PRD.xtc -o trajwhole.xtc gmx trjconv -pbc nojump -s PRD.tpr -f trajwhole.xtc -o trajcluster.xtc gmx trjconv -pbc mol -center -s PRD.tpr -f

Re: [gmx-users] DSSP

t; J > > On Tue, Dec 5, 2017 at 3:41 PM, Vidya R <vidyadevi2...@gmail.com> wrote: > > > I got the error > > > > dssp cmd='/usr/local/bin -i ddpEbgmY -o ddtFRo32 > /dev/null 2> > /dev/null' > > Reading fra

Re: [gmx-users] DSSP

mailed Maarten at "m.hekkel...@cmbi.ru.nl" but I'm not sure this > email is active anymore. Hopefully it is, otherwise please let me know. > > Best regards, > J > > On Tue, Dec 5, 2017 at 6:38 AM, Vidya R <vidyadevi2...@gmail.com> wrote: > > > Hi gro

[gmx-users] DSSP

Hi gromacs users, I use gromacs 5.1.4 in *cygwin* (OS windows 7, 64 bit.) I want to download and install dssp tool. How to proceed? Thanks, Vidya.R -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

[gmx-users] BONDS BREAK DURING MINIMIZATION

Hi gromacs users, The bonds of my organic molecule, break while computing rdf. The following sentences appear while first minimization Step 11, time 0.011 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.02, max 0.79 (between atoms 20 and 6) bonds that rotated more

[gmx-users] fixing molar concentrations in gromacs

Hi gmx users, I want to consider one organic molecule of solute dissolved in several molecules of water. How to fix molar concentrations in gromacs ? ( say 0.1 M ) Thanks, Vidya.R -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

whatever quirks exist with SGE are unfortunately between you, its docs and > your cluster's docs and admins :-( > > Mark > > On Sun, Sep 17, 2017 at 7:23 AM Vidya R <vidyadevi2...@gmail.com> wrote: > > > My log file is provided in the link below > > > > C

Re: [gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

https://drive.google.com/file/d/0BxGqxeGwTDLbLWJ5SExDblVhRFU /view?usp=sharing=59be86ad On Sun, Sep 17, 2017 at 6:35 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/17/17 1:22 AM, Vidya R wrote: > >> My log file is provided in the link below >> >> Ca

[gmx-users] gromacs-error.docx

I've shared an item with you: gromacs-error.docx https://drive.google.com/file/d/0BxGqxeGwTDLbLWJ5SExDblVhRFU/view?usp=sharing=59be86ad It's not an attachment -- it's stored online. To open this item, just click the link above. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

My log file is provided in the link below Can you please look into it and let me know why the error arises? I am feeding my commands in SGE cluster. When I run it in my login node, gmx mdrun -v -deffnm eql runs well But, through qsub command, (with 8 processors) It says, mpirun noticed that

[gmx-users] what is the difference between gmx mdrun and gmx tune_pme

Hi gromacs users, What is the difference between gmx mdrun and gmx tune_pme? Which is better to use in a cluster (especially when we submit our jobs through qsub command?) Also, what is the purpose of -np option in gmx tune_pme? Can someone elucidate? Thanks, Viday.R -- Gromacs Users

[gmx-users] gmx tune_pme

Hi gromacs users, When i tried using, gmx tune_pme -np 8 -s eql2.tpr -launch Got this error.. How to fix it? [compute-0-3.local:28193] [[20294,1],0] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file rml_oob_send.c at line 105

[gmx-users] how to fix pme number

Hi gromacs users, In this command, gmx mdrun -ntmpi 1 -ntomp 8 -v -deffnm eql2 how to determine the value of pme.. I want to include -npme... Please help Thanks, Vidya.R -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] gromacs error

ted since. > Since a rebuild is the way to investigate that, definitely update to at > least the latest 5.0.x while you do it. > > Mark > > On Mon, Sep 11, 2017 at 3:36 PM Wes Barnett <w.barn...@columbia.edu> > wrote: > > > On Mon, Sep 11, 2017 at

Re: [gmx-users] error sharing libraries...gromacs error

use the > C++ performance is very poor. We recommend latest gcc or intel. > > Otherwise, configure GROMACS so that it uses the wrapper compilers when > buildling, e.g. cmake -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpic++ > etc. Organizing this stuff is their job. > > Ma

[gmx-users] error sharing libraries...gromacs error

Hi, I give these commands PATH=$PATH:"/usr/local/gromacs/bin/" export GMXLIB=/usr/local/gromacs/share/gromacs/top export LD_LIBRARY_PATH=/usr/lib export MPIRUN="/usr/mpi/pgi/openmpi-1.2.8/bin/mpirun" export

[gmx-users] gromacs error

Hi, When I give these two commands gmx grompp -f mdp/min.mdp -o min -pp min -po min gmx mdrun -deffnm min I get this error. What to do? Reading file min.tpr, VERSION 5.0.2 (single precision) tMPI error: tMPI Initialization error (in valid comm) Thanks, Vidya.R -- Gromacs Users mailing

[gmx-users] GETTING GOOD PERFORMANCE FROM MDRUN

Hi, How to get good (and fast) performance from mdrun through available 8 logical CPU cores? When I gave, gmx mdrun -ntmpi 2 -ntomp 4 -v -deffnm eq It seems to be slow, much slower than gmx mdrun -v -deffnm eq. Can anyone help? Thanks, Vidya R -- Gromacs Users mailing list * Please search

[gmx-users] TOPOLOGY USING OPLS FORCEFIELD

Hi gromacs users, After getting the output from topolbuild, how to construct topology file using opls forcefield? Can anyone send useful links for the same? Thanks, Vidya.R -- Gromacs Users mailing list * Please search the archive at

[gmx-users] compiling ambconv

Hi gromacs users, How to compile ambconv extracted from ambconv.tgz? Thanks, Vidya R -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] RDF

Hi, I want to calculate RDF of my organic molecule with a solvent. What should be the duration of my simulation? Is 100 ps enough? Thanks, Vidya.R -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *