[gmx-users] Large VCM error for a POPC bilayer simulation : 2ndattempt

[Justin A. Lemkul]

> > > ##########
> > > 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
> > >
> > > ##########
> > >
> > >
> > > ------------------------------------------------------------------------
> > >
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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
> > http://www.bioinf.uni-sb.de/RB/
> > ___________________________________________________________
> >
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>



======================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/

======================