Thank all of you for the suggestions! I then ran the procedures described at (http://www.nmr.chem.uu.nl/~abonvin/tutorials/MD-Data/index.html), where it adds water before energy minimization, and it also has position restraint step. But when I came to the step:
grompp -f dyna/pr1_SOLV.mdp -po X_pr1.mdp -c X_em3.gro -r X_em3.gro -t X_em3.trr -n X.ndx -p X.top -o X_pr1.tpr mdrun -v -deffnm X_pr1 I got the following error: ------------------------------------------------------- Program mdrun, VERSION 3.3.2 Source code file: network.c, line: 437 Routine should not have been called: gmx_sumi ------------------------------------------------------- I used exactly the same .mdp files as in the tutorial, with the only modification in pr1.mdp to set T-coupling to "Protein Non-Protein". Does anybody know what might be the problem? Thanks! Peggy On Nov 19, 2007 3:41 AM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > Quoting liang <[EMAIL PROTECTED]>: > > > > Never couple solvent and ions separately. Check out: > > > > > http://wiki.gromacs.org/index.php/Thermostats > > > > > Try tc-grps = Protein Non-protein > > > > excuse me, if the system includes lipid bilayer, how should i set the > > tc-prgs? > > Protein + Lipids + Sol and Ion? > > or Protein + Non-protein ? > > I think either would work, but I've personally used protein, lipids, solvent + > ions. As long as you're not coupling a very small amount of atoms/ions to its > own bath then you should avoid problems. > > -Justin > > > > > thanks > > > > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > [EMAIL PROTECTED] | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > ======================================== > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php