[gmx-users] Large VCM and mdrun crashed

[Tsjerk Wassenaar]

Hi Xie Yinghong,

When simulating under periodic boundary conditions, mdrun constantly chooses
the best copy of each molecule for reference, giving rise to jumps over the
boundaries. When you have a number of large molecules, the COM of these
together may jump quite a bit, if one of the proteins jumps. It is better to
select one group consisting of small parts, such as the solvent or a lipid
bilayer, or one of the larger molecules in your system for VCM removal to
avoid jumps in the COM.

Cheers,

Tsjerk


On 10/12/05, David <spoel at xray.bmc.uu.se> wrote:
>
> On Wed, 2005-10-12 at 12:10 -0800, Yinghong wrote:
>
> > Because in my system, several protein chains are included. So, Did I
> > need to make C.O.M removal for every seperated group? For example, is
> > it ok for me to define "comm_grps = Protein1 Protein2 Protein3"?
> >
> You only want to do this in very special cases like
> membrane/protein/water systems. Here you want just one group.
>
>
> >
> >
> > Thanks in advance.
> >
> >
> >
> >
> >
> > Xie Yinghong
> >
> > Hong Kong Univ.
> >
> > _______________________________________________
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> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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