Hi, Thanks for the help. I did not know about this function.
However, genconf seems to be another way of building the system from scratch all over again. (step 1 of my previous email). I think I have a fairly reasonable system before starting dynamics, although the replication of the 128-lipid assembly was not done using genconf. I was wondering how to get past the large VCM error ? Thank you -Himanshu On 10/17/07, Rainer Böckmann <[EMAIL PROTECTED]> wrote: > > Hi, > > genconf -nbox 2 2 1 > > will help you. > > Best, > rainer > > > himanshu khandelia wrote: > > Hi, > > > > My message did not go through properly to the mailing list (only the > > attachment went through). Here is a repeat attempt: > > > > ########## > > 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) > > > > - 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) > > > > 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 >
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