Hi,<br><br>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.<br><br>If this does not work, I will try editconf. <br><br>Thank you all for the comments and help,
<br><br>-Himanshu<br><br><div><span class="gmail_quote">On 10/17/07, <b class="gmail_sendername">Justin A. Lemkul</b> <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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;">
> > > ##########<br>> > > Hi Folks,<br>> > ><br>> > > I was trying to make a large POPC system from Tieleman's 128 lipid<br>> > 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)<br>> > 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<br>> > VMD),<br>> > > and translated replicas along the bilayer plane accordingly<br>> > >
<br>> > > - to remove bad contacts, minimized it in GROMACS (steep minimization)<br><br>Rainier's suggestion is a good one; I would echo it for ease of use. Did your<br>minimization end properly (i.e., converge to a nice negative potential energy)?
<br><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>Are you freezing these molecules (using freezegrps in the .mdp)? I believe the
<br>combination of pressure coupling and frozen dimensions is incompatible, but I<br>could be wrong and will defer to anyone more experienced than I if so. You<br>might be introducing some nasty collisions. Have you tried running a short NVT
<br>simulation to try to relax your solvent? That might help as well.<br><br>-Justin<br><br>> > ><br>> > > In the last step, the system crashes after a few hundred steps,<br>> > reporting a<br>> > > large VCM. A look at the pdb files reveals that the system is exploding
<br>> > with<br>> > > large vacuum regions appearing.<br>> > ><br>> > > THE BOX CENTER WAS VERY FAR FROM THE GEOMETRIC ORIGIN. The box is ~ 13<br>> > 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<br>> > 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>> > >
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</a><br>> ><br>><br><br><br><br>======================<br><br>Justin A. Lemkul<br>Graduate Research Assistant<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br><a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu
</a> | (540) 231-9080<br><a href="http://bevanlab.biochem.vt.edu/Pages/Personal/justin/">http://bevanlab.biochem.vt.edu/Pages/Personal/justin/</a><br><br>======================<br>_______________________________________________
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