[gmx-users] NPT MD and Berendsen

Chetan Mahajan chetanvm10 at gmail.com
Mon Jun 23 07:53:19 CEST 2014

By space in second part of the email, I meant vacuum.

On Mon, Jun 23, 2014 at 12:50 AM, Chetan Mahajan <chetanvm10 at gmail.com>

> Dear All,
> I am using Berendsen barostat and thermostat for NPT equilibration MD run
> at 1 atm and 300 K. While it runs fine, average pressure at the end of the
> run is 19 bar. I am confused whether this is way off 1 atm target, or is
> justified recalling gromacs manual that says Berendsen barostat does not
> yield correct thermodynamic ensemble.
> IN addition, initial box elongates to have space at both ends in
> z-direction as can be seen in following link:
> https://www.dropbox.com/sh/dahnyy3zy6vb1xh/AAD5ppxrm18rB3DHZ0Qji0qva
> Again, I am not sure if this is a case for concern or just artifact of
> using Berendsen.
> Is Parrinello-Rahman better than Berendsen, even for initial NPT
> equilibration?
> Thanks
> Chetan

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