[gmx-users] Large VCM and mdrun crashed
tsjerkw at gmail.com
Wed Oct 12 13:56:25 CEST 2005
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.
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 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
9747AG Groningen, The Netherlands
+31 50 363 4336
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