[gmx-users] pme + barostat

[Anton Feenstra]

Valentin Gogonea wrote:
> 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.
[...]
> rlist               =  0.5
> rcoulomb            =  0.5
> rvdw                =  0.5

Your cut-offs (even with pme) seem insensibly short to me. In any case
you will be neglecting vdw interactions beyond 5 Angstroms, which is bad!
But also PME coulomb may not be accurate enough at those short distances.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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