Position restraints in Parrinello-Rahman pressure coupling

User discussions
1

GROMACS version: 2020.1
GROMACS modification: No

Dear all,

I have to use position restraint for the film-like part of a system of under study.

After equilibration, I would like to run the production/data collection step in NPT ensemble where I have two possibilities of Berendsen and Parrinello-Rahman to couple the pressure by which.

Using the Parrinello-Rahman leads the system to instabilities as it has been combined with position restraints. The Gromacs also warns about such combinations and recommends to use the Berendsen barostat instead.

In another side, the Berendsen barostat produces an invalid statistical mechanical ensemble and should never be employed during data collection according to an old comment from Justin in the mailing list.

So, which barostat would you kindly recommend to use for such a system?

Thank you,
Salman

2

If the system is adequately equilibrated, the combination of restraints and Parrinello-Rahman shouldn’t be an issue. The most common use of restraints is in equilibration, for which Parrinello-Rahman would be inappropriate. But if the system is stable, there shouldn’t be a problem.

3

Thank you Justin for your response.
If there is any, I would so appreciated if you could kindly address me to one or two references in which the drawbacks of using (in data collection) the Berendsen barostat have been addressed.

Thank you

4

See http://dx.doi.org/10.1007/b99427 and references therein.