Re: [gmx-users] flexible organic solvents

Hi, additionally to the remaks of Andreas there are some parameters in the GROMOS force field G53a5/6 for the solvents you want to simulate (see the original paper). A good read of chapter five of the manual and to all the files in the $GMX/share/top directory should let you build those models

Re: [gmx-users] tfe.itp

shahrbanoo karbalaee wrote: Dear justin I made topology top for tfe with gromos53a5.and I solvated in spc and 40molecule tfe.I includeed tfe.itp in topology.but when I do grompp I get this error.(I edit the name of atoms with name in rtp file HT) Generated 165 of the 1596 non-bonded parameter

[gmx-users] FFTW & Gromacs installation on AIX 5.3

Hi, Earlier i had faced problems installing FFTW on IBM p595. Thankfully now I had found out that they were already installed and I assumed they weren't: [EMAIL PROTECTED]:~/gromacs-3.3.3$ ls -al /applic/local/lib/libfftw3.* -rw-r--r-- 1 applic in0007 2507094 Nov 12 2007 /applic/local/li

Re: [gmx-users] FFTW & Gromacs installation on AIX 5.3

We recently ran into this issue, and it was solved by re-compiling FFTW in single precision. I would suggest talking to your sysadmin to see if you can get the right precision compiled. Not a bad idea to have both single and double precision available to you, anyway :) -Justin Senthil Kumar

Re: [gmx-users] New Gromacs-CPMD QMMM webpage

  dear sir,     i am vidhya sankar speaking . i am not able to down load QM/MM exampiles files since it take much time and huge memory (156Mb) often net is disconnected could you please send some example input files of CPMD part  mainly 'CPMD_inp.tmpl'  'runcpmd' ? please i am expectin

[gmx-users] MDRUN with MPIRUN

Hi There, I am trying to run the gromacs with mpirun, but don't know the exact commands for running gromacs with mpirun. If, somebody can give the exact command to run mdrun with MPI. It will be of great help for me to do my job. Thanks in advance, Vivek ___

[gmx-users] FFTW & Gromacs installation on AIX 5.3

Hi Senthil, here is how I have compiled fftw and gromacs on an AIX. A warning though that the gromacs compilation usin the xlc_r compiler set took over 12h. First fftw: [EMAIL PROTECTED]:/hpf/data/pomes/cneale/exe/fftw-3.1.2_aix> cat cn_compile.sh #!/bin/bash export PATH=/usr/vac/bin:/usr/va

Re: [gmx-users] FFTW & Gromacs installation on AIX 5.3

ls -l /applic/local/lib/libfftw* should see libfftw3f.a there (libfftw3.a is the double precision, libfftw3f.a is the single precision fftw3 lib) export LIBS='-L/applic/local/lib -lfftw3f' ./configure ... Senthil Kumar M wrote: > Hi, > > Earlier i had faced problems installing FFTW on IBM

RE: [gmx-users] MDRUN with MPIRUN

mpirun -np mdrun various options... -np (all in one line) > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of vivek sharma Sent: 20 August 2008 12:44 To: Discussion list for GROMACS users Subject: [gmx-users] MDRUN with MPIRUN Hi There, I am trying to run the gromacs with mpi

Re: [gmx-users] MDRUN with MPIRUN

Hi, Thanks for your reply. Do you have any idea of how to run commands using scheduler command "bsub" With Thanx, Vivek 2008/8/20 Kukol, Andreas <[EMAIL PROTECTED]> > mpirun -np mdrun various options... -np processors> > > (all in one line) > > > > From: [EMAIL PROTECTED] [mailto:[EMAIL P

[gmx-users] rb1 test failed after recompiling gromacs 3.3.2

Hello, I've run the gmxtest on Gromacs-3.3.2. One simple test failed: Testing rb1 . . . *** glibc detected *** realloc(): invalid next size: 0x082c0180 *** sh: line 1: 27398 Aborted mdrun >mdrun.out 2>&1 FAILED. Check files in rb1 And two complex tests failed as wel

Re: [gmx-users] Using Morse potentials with ENCAD force field

Actually I think I am using the gromos force field. I have been using Christopher Stiles page as a guide to get started with using CNT http://cs86.com/CNSE/SWNT.htm. I realize now that all the modifications were made to ffgmx files. So I believe I am using the gromos forcefield. Is the forcefield

[gmx-users] AFM and g_wham

Dear users: When I finished a AFM simulation and wanted to analyze the pdo file ,but g_wham can not run and report errors ,such as :"This does not appear to be a valid pdo file" or "You need to specify a series of pdo files as input", and mailing lists can not give me correct anwser. Please he

[gmx-users] Simulations backward in time.

Hi, I wanted to perform some simulations backward and forward in time (for transition path sampling ). If I specify a negative value for 'dt' in the mdp file, would that work for backward integration of the equations of motion ? Thanks Sumanth N Jamadagni Graduate Student Isermann Dept of

[gmx-users] tfe.itp

Dear justin after edit tfe.itp , I did the command grompp and I got this error : error input solvated.gro. Do I have to make spc.gro with tis forcefield(gromos965a)? best -- sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http:/

[gmx-users] The WARNING

HI WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Is this warning serious? Could any one tell me how to fix the warning? I see nothing wrong with my .top and my .gro file. Thank you Lin

Re: [gmx-users] The WARNING

Chih-Ying Lin wrote: HI WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Is this warning serious? Could any one tell me how to fix the warning? use a tpr file. I see nothing wrong with my .top and my .gro file.

Re: [gmx-users] Simulations backward in time.

Sumanth Jamadagni wrote: Hi, I wanted to perform some simulations backward and forward in time (for transition path sampling ). If I specify a negative value for 'dt' in the mdp file, would that work for backward integration of the equations of motion ? Have you tried? If yes, what happened

[gmx-users] pdb file ???

Hi It is the water-molecule system. For a molecule, like R-N(CH3)3-Br, I could make a pdb file either include Br ion or exclude Br ion. If I exclude Br ion, I have to make Br ion as the counter ion for my system. If I include Br ion, I do NOT have to make Br ion as the counter ion since it will