[gmx-developers] dispersion correction / exploding box
spoel at xray.bmc.uu.se
Mon Aug 22 21:31:52 CEST 2005
On Mon, 2005-08-22 at 18:42 +0200, Rainer Böckmann wrote:
> 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)
> 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.'
Can you give more details? Dispersion energy, VDW treatment and cut-offs etc.
> Any ideas?
> Thanks & best wishes,
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
More information about the gromacs.org_gmx-developers