[gmx-users] pme + barostat

[Pim Schravendijk]

> 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.
> 
> Valentin