[gmx-developers] dispersion correction / exploding box

[Rainer Böckmann]

Dear All:

we experienced a very fast (~10-50ps) increasing/exploding box for a 
system of approx. 100,000 atoms using the OPLS forcefield, TIP4 water, 
and a dodecahedron box aready during position restraint runs (restraints 
on the protein). Further options:

gromacs 3.3, cvs version (download ~3 weeks ago)
PME
energy/pressure dispersion correction switched on
310 K, 1bar

We observe this behaviour only for certain box sizes/proteins, e.g. the 
box explodes using a distance of 1.4nm or 1.5nm  between the protein and 
the box but not for 1.2nm. It is not dependent on the PME parameters, 
but at least partly on the dispersion correction term. The box appears 
to be stable without the dispersion correction.

Any ideas?

Thanks & best wishes,
Rainer

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Dr. Rainer Böckmann
Theoretical & Computational Membrane Biology
Center for Bioinformatics Saar
Universität des Saarlandes
Gebäude 17.1, EG
D-66041 Saarbrücken, Germany
Phone: ++49 +681 302-64169  FAX: ++49 +681 302-64180
E-Mail: rainer at bioinformatik.uni-saarland.de
http://www.bioinf.uni-sb.de/RB/
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