Hi,<br><br>Thanks for the help. I did not know about this function. <br><br>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.
<br><br>I was wondering how to get past the large VCM error ? <br><br>Thank you <br><br>-Himanshu<br><br><div><span class="gmail_quote">On 10/17/07, <b class="gmail_sendername">Rainer Böckmann</b> <<a href="mailto:rainer@bioinformatik.uni-saarland.de">
rainer@bioinformatik.uni-saarland.de</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi,<br><br>genconf -nbox 2 2 1<br>
<br>will help you.<br><br>Best,<br>rainer<br><br><br>himanshu khandelia wrote:<br>> Hi,<br>><br>> My message did not go through properly to the mailing list (only the<br>> attachment went through). Here is a repeat attempt:
<br>><br>> ##########<br>> Hi Folks,<br>><br>> I was trying to make a large POPC system from Tieleman's 128 lipid assembly.<br>> Everything went well until I tried to run dynamics. While trying to run
<br>> dynamics, I got a large velocity for the center of mass (Large VCM) error.<br>> The log file, mdp file, and the top file are attached as a suse .zip<br>><br>> Here is what I did:<br>><br>> - replicated the system thrice to make is 512 lipids (this was done in VMD),
<br>> and translated replicas along the bilayer plane accordingly<br>><br>> - to remove bad contacts, minimized it in GROMACS (steep minimization)<br>><br>> - to remove bad contacts farther, minimized using CG
<br>> (The system looks fairly reasonable after minimization on visual<br>> inspection)<br>><br>> - tried to assign velocities at 50 K and run NPT dynamics, with water<br>> molecules constrained along the bilayer normal (z)
<br>><br>> In the last step, the system crashes after a few hundred steps, reporting a<br>> large VCM. A look at the pdb files reveals that the system is exploding with<br>> large vacuum regions appearing.<br>
><br>> THE BOX CENTER WAS VERY FAR FROM THE GEOMETRIC ORIGIN. The box is ~ 13 x 13<br>> x 6.7, and the center is at 6.3, 6.3, 3.5. So I also tried the following<br>> before running dynamics:<br>><br>> - used editconf -c to center the box, before running dynamics. But this only
<br>> moved the center by less than 5 angstroms. Why ?<br>> - used editconf -c -center 0 0 0 as a variant of the above.<br>><br>> The above did not solve the problem.<br>> Please let me know if you want me to send you more details ?
<br>><br>> Thanks for the help,<br>><br>> -Himanshu<br>> MEMPHYS,<br>> SDU, Denmark<br>><br>> ##########<br>><br>><br>> ------------------------------------------------------------------------
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</a><br><br><br>--<br>__________________________________________________________<br>Dr. Rainer Böckmann<br>Theoretical & Computational Membrane Biology<br>Center for Bioinformatics Saar<br>Universität des Saarlandes<br>
Gebäude C7.1 (17.1), EG<br>D-66041 Saarbrücken, Germany<br>Phone: ++49 +681 302-64169 (68666) FAX: ++49 +681 302-64180<br>E-Mail: <a href="mailto:rainer@bioinformatik.uni-saarland.de">rainer@bioinformatik.uni-saarland.de
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