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

[himanshu khandelia]

Hi,

Thanks for the help. I did not know about this function.

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.

I was wondering how to get past the large VCM error ?

Thank you

-Himanshu

On 10/17/07, Rainer Böckmann <rainer at bioinformatik.uni-saarland.de> wrote:
>
> Hi,
>
> genconf -nbox 2 2 1
>
> will help you.
>
> Best,
> rainer
>
>
> himanshu khandelia wrote:
> > Hi,
> >
> > 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
> > inspection)
> >
> > - 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,
> >
> > -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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