Re: [gmx-users] Q's about adding bonded interaction

Frankie Montenegro wrote: Hi everyone, */I have posted these few questions on the developers list few days ago but didn't get any feedback. I'd really appreciate some input, I am quite lost in gromacs (not so small) source tree. /* I am trying to add a two-body bonded interaction, following a "

[gmx-users] Q's about adding bonded interaction

Hi everyone, *I have posted these few questions on the developers list few days ago but didn't get any feedback. I'd really appreciate some input, I am quite lost in gromacs (not so small) source tree.* I am trying to add a two-body bonded interaction, following a "list of files to modify", given

Re: [gmx-users] problems with gromacs tools under certain compilations

Grace Li wrote: Hi Gromacs users: I was wondering if anyone has ran into the type of a problem where, you're running a gromacs analysis tool, for example g_dist g_dist -f traj.xtc -s traj.tpr -n index and half way through reading frames, it just stops and hangs and does not do anything at

Re: [gmx-users] asymmetric distribution of water

pragya chohan wrote: hi ... i want to start a simulation with asymmetric distribution of water on the bilayer (upper leaftlet having more and lower one less). has anyone ever encountered a paper with such a simulation. Is it possible? Only when you don't use periodic boundary conditions. Then of

[gmx-users] asymmetric distribution of water

hi ... i want to start a simulation with asymmetric distribution of water on the bilayer (upper leaftlet having more and lower one less). has anyone ever encountered a paper with such a simulation. Is it possible? Thanks for any help __

[gmx-users] problems with gromacs tools under certain compilations

Hi Gromacs users: I was wondering if anyone has ran into the type of a problem where, you're running a gromacs analysis tool, for example g_dist g_dist -f traj.xtc -s traj.tpr -n index and half way through reading frames, it just stops and hangs and does not do anything at all. I have ran into

Re: [gmx-users] energy minimization of a bilayer

Ananya Debnath wrote: Hi, I am a recent user of Gromacs. I tried to make initial configuration of a bilayer in united atom model having Btmac, Stearyl alcohol and water with packmol and then energy minimization with gromacs. Initially I made a bilayer with gromos87 forcefield, ffgmx.itp, and tha

Re: [gmx-users] regarding .gro file

Ananya Debnath wrote: Hi, Can anyone tell me whether gromacs writes coordinate in .gro file with periodic boundary condition? The coordinates are the coordinates. Whether you choose to interpret them modulo some box is up to you and the software. Is this really the question you meant to ask

RE: [gmx-users] regarding .gro file

In the last line. Dr. Yuguang Mu School of Biological Sciences 60 Nanyang Drive Nanyang Technological Uiversity Singapre Tel: +65-63162885 email:ygmuATntu.edu.sg -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ananya Debnath Sent: Friday, November 23, 20

[gmx-users] regarding .gro file

Hi, Can anyone tell me whether gromacs writes coordinate in .gro file with periodic boundary condition? Thanks, Ananya. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] problem with mdrun performing replica exchange MD

On Fri, 23 Nov 2007 12:42:45 +0100 "Xavier Periole" <[EMAIL PROTECTED]> wrote: David is write, you need to rename the tpr files is the following cmd: well, I believe David was right not write :)) mpirun -np 8 mdrun_mpi -s XXX.tpr -replex 2500 -reseed -1 -multi 8 by XXX0.tpr XXX1.ptr ... X

Re: [gmx-users] problem with mdrun performing replica exchange MD

David is write, you need to rename the tpr files is the following cmd: mpirun -np 8 mdrun_mpi -s XXX.tpr -replex 2500 -reseed -1 -multi 8 by XXX0.tpr XXX1.ptr ... XXX7.tpr This time I used the following command line: mpirun -np 8 mdrun_mpi -s simul0.tpr -replex 2500 -reseed -1 -multi 8.

Re: Re: RE: [gmx-users] problem with mdrun performing replicaexchange MD

No, David gave a confusing hint. If you files are called simul0.tpr simul1.tpr etc. you should use mdrun -s simul.tpr mdrun will add the numbers. With 3.3 you do not need the multi option and -multi does not take an argument (but incorrect command line options to mdrun will be ignored). My ori

Re: Re: RE: [gmx-users] problem with mdrun performing replica exchange MD

This time I used the following command line: mpirun -np 8 mdrun_mpi -s simul0.tpr -replex 2500 -reseed -1 -multi 8. I got the following error: Program mdrun_mpi, VERSION 3.3.99_development_20070413 Source code file: gmxfio.c, line: 706 Can not open file: simul0_md0.tpr

Re: [gmx-users] problem with mdrun performing replica exchange MD

OZGE ENGIN wrote: This time, I used the following command line: mpirun -np 8 mdrun_mpi -s simul0_md.tpr -replex 2500 -reseed -1 -multi 8 rename rename your tpr files to simul_md0.tpr simul_md1.tpr ... simul_md7.tpr but I got the following error: Program mdrun_mpi, VERSION 3.3.99_developmen

Re: Re: RE: [gmx-users] problem with mdrun performing replica exchange MD

This time, I used the following command line: mpirun -np 8 mdrun_mpi -s simul0_md.tpr -replex 2500 -reseed -1 -multi 8 but I got the following error: Program mdrun_mpi, VERSION 3.3.99_development_20070413 Source code file: gmxfio.c, line: 706 Can not open file: simul00.tpr -

[gmx-users] energy minimization of a bilayer

Hi, I am a recent user of Gromacs. I tried to make initial configuration of a bilayer in united atom model having Btmac, Stearyl alcohol and water with packmol and then energy minimization with gromacs. Initially I made a bilayer with gromos87 forcefield, ffgmx.itp, and that worked fine. With same

Re: RE: [gmx-users] problem with mdrun performing replica exchange MD

You need to supply the -np option. In Gromacs 3.3 you don't need to set the -multi option, and -multi does not take an argument. If you use the CVS head branch, you need to set -np and -multi both with an argument. Berk. From: "OZGE ENGIN" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMA

Re: RE: [gmx-users] problem with mdrun performing replica exchange MD

Hi Berk, I indicated the number of replicas with -multi option. In additon, I have compiled Gromacs with MPI support. I used the following command line: mdrun -s simul0.tpr -multi 16 -reseed -1 -replex 2500 -Original Message- From: "Berk Hess" <[EMAIL PROTECTED]> To: gmx-users@gromacs.

RE: [gmx-users] problem with mdrun performing replica exchange MD

From: "OZGE ENGIN" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: [gmx-users] problem with mdrun performing replica exchange MD Date: Fri, 23 Nov 2007 11:30:53 +0200 Hi All, I am performing replica exchange molecular dynamics simulation(RE

[gmx-users] problem with mdrun performing replica exchange MD

Hi All, I am performing replica exchange molecular dynamics simulation(REMD). I have 16 replicas each of which has a peptide with different conformation. After obtaining .tpr files (at desired temperatures) for each replicas, I loaded them via mdrun, but I got the following error: Fatal error: