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

[himanshu khandelia]

Hi,

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.

If this does not work, I will try editconf.

Thank you all for the comments and help,

-Himanshu

On 10/17/07, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
> > > > ##########
> > > > 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/
>
> ======================
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