[gmx-users] pme + barostat
schraven at mpip-mainz.mpg.de
Thu Aug 12 02:17:11 CEST 2004
> rlist = 0.5
> rcoulomb = 0.5
> rvdw = 0.5
Your box size may be too small, make sure that your solute can't see
itself in a periodic image within one cut-off distance also cut-offs of
0.5 are on the low side, you'd better go to the default values (0.8 for
rlist and and something like 1.2 for rcouloumhb/rvdw, if I remember well,
check the manual).
> Dear gromacs users,
> I am trying to run a short simulation of a small organic molecule in
> water. When I use PME with Parrinello-Rahman barostat the density
> changes dramatically and wholes appear in the simulation box. This
> doesn't happen when I replace PME with cutoff.
> Did anybody experience this problem and how can I get it fixed?
> Thank you for your help.
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