[gmx-users] NPT MD and Berendsen

[Francis Jing]

How long was the average taken over? If the error is larger than the
pressure itself, you cannot make judgment.
Generally Berendsen is only inaccurate about the fluctuations, not the mean
value.


Francis


On Mon, Jun 23, 2014 at 1:50 PM, 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
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-- 
Zhifeng (Francis) Jing
Graduate Student in Physical Chemistry
School of Chemistry and Chemical Engineering
Shanghai Jiao Tong University
http://sun.sjtu.edu.cn