[gmx-users] Large VCM error for a POPC bilayer simulation : 2nd attempt
rainer at bioinformatik.uni-saarland.de
Wed Oct 17 13:43:36 CEST 2007
genconf -nbox 2 2 1
will help you.
himanshu khandelia wrote:
> 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
> - 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,
> SDU, Denmark
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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: rainer at bioinformatik.uni-saarland.de
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