[gmx-users] tfe.itp

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 combinations ERROR 0 [file

Re: [gmx-users] REMD trjcat -demux problem

Di Pan wrote: Hi, everyone: I met a problem when I try to use the trjcat -demux to connect trajectory files of REMD. I use 68 replicas for REMD simulation, and use demux.pl script to get the replica_index.vgx file. Then I try to use the trjcat -f traj*.xtc -demux replica_index.xvg to get a

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

Andy Shelley wrote: I have added a mixture of oxgen and nitrogen to a simulation with a cnt. The oxygen and nitrogen use morse potentials and the cnt uses the encad force field. Previously I simulated the cnt with the default water and it worked well. When using my air mixture the cnt

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

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

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

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

[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

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 number of processors mdrun various options... -np number of processors (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

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 number of processors mdrun various options... -np number of processors (all in one line) From: [EMAIL PROTECTED]

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] 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