Hi, The simulation does not explode if I run in NVT for 5000 steps. I am running a longer simulation now, and will update the post.
If this does not work, I will try editconf. Thank you all for the comments and help, -Himanshu On 10/17/07, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > > > > ########## > > > > Hi Folks, > > > > > > > > I was trying to make a large POPC system from Tieleman's 128 lipid > > > assembly. > > > > Everything went well until I tried to run dynamics. While trying to > run > > > > dynamics, I got a large velocity for the center of mass (Large VCM) > > > error. > > > > The log file, mdp file, and the top file are attached as a suse .zip > > > > > > > > Here is what I did: > > > > > > > > - replicated the system thrice to make is 512 lipids (this was done > in > > > VMD), > > > > and translated replicas along the bilayer plane accordingly > > > > > > > > - to remove bad contacts, minimized it in GROMACS (steep > minimization) > > Rainier's suggestion is a good one; I would echo it for ease of use. Did > your > minimization end properly (i.e., converge to a nice negative potential > energy)? > > > > > > > > > - to remove bad contacts farther, minimized using CG > > > > (The system looks fairly reasonable after minimization on visual > > > > inspection) > > > > > > > > - tried to assign velocities at 50 K and run NPT dynamics, with > water > > > > molecules constrained along the bilayer normal (z) > > Are you freezing these molecules (using freezegrps in the .mdp)? I > believe the > combination of pressure coupling and frozen dimensions is incompatible, > but I > could be wrong and will defer to anyone more experienced than I if > so. You > might be introducing some nasty collisions. Have you tried running a > short NVT > simulation to try to relax your solvent? That might help as well. > > -Justin > > > > > > > > > In the last step, the system crashes after a few hundred steps, > > > reporting a > > > > large VCM. A look at the pdb files reveals that the system is > exploding > > > with > > > > large vacuum regions appearing. > > > > > > > > THE BOX CENTER WAS VERY FAR FROM THE GEOMETRIC ORIGIN. The box is ~ > 13 > > > x 13 > > > > x 6.7, and the center is at 6.3, 6.3, 3.5. So I also tried the > following > > > > before running dynamics: > > > > > > > > - used editconf -c to center the box, before running dynamics. But > this > > > only > > > > moved the center by less than 5 angstroms. Why ? > > > > - used editconf -c -center 0 0 0 as a variant of the above. > > > > > > > > The above did not solve the problem. > > > > Please let me know if you want me to send you more details ? > > > > > > > > Thanks for the help, > > > > > > > > -Himanshu > > > > MEMPHYS, > > > > SDU, Denmark > > > > > > > > ########## > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > > _______________________________________________ > > > > 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 > > > > > > > > > -- > > > __________________________________________________________ > > > Dr. Rainer Böckmann > > > Theoretical & Computational Membrane Biology > > > Center for Bioinformatics Saar > > > Universität des Saarlandes > > > Gebäude C7.1 (17.1), EG > > > D-66041 Saarbrücken, Germany > > > Phone: ++49 +681 302-64169 (68666) FAX: ++49 +681 302-64180 > > > E-Mail: [EMAIL PROTECTED] > > > http://www.bioinf.uni-sb.de/RB/ > > > ___________________________________________________________ > > > > > > _______________________________________________ > > > 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 > > > > > > > > > ====================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > [EMAIL PROTECTED] | (540) 231-9080 > http://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 >
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