[gmx-users] NPT MD and Berendsen

[Chetan Mahajan]

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


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

> 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
>