[gmx-users] NPT MD and Berendsen

[Chetan Mahajan]

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