[gmx-users] anisotropic pressure coupling
David van der Spoel
spoel at xray.bmc.uu.se
Tue Oct 1 14:24:52 CEST 2002
On Tue, 2002-10-01 at 13:57, A. und B. Nick wrote:
> I want to run a variable shape MD simulation on a box of
> 3120 CH2 groups belonging to 20 chains (box size=4,5nm).
> The structure was preequilibrated with MC and I run about
> 1,5 ns MD with isotropic boundary conditions for further
> After switching to anistropic pressure coupling I always
> run into problems and the job crashes after a while.
> The error messages are: "too skrewed box" when I use
> LINCS for bond contraints or I recieve a segmentation
> fault if I run the job without any contraints.
> Does anyone know how to overcome this problem?
You may want to turn on the analytic correction for LJ:
dispcorr = EnerPres
and then set your ref_p to 1.
Otherwise I can only think of even longer tau_p, and/or slightly longer
cut-off (1.2, or even twin range 0.9/1.4)
Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
More information about the gromacs.org_gmx-users