[gmx-users] Re: the Pressure control in GROMACS 4.0.7

Vitaly Chaban vvchaban at gmail.com
Sat Jul 10 09:47:40 CEST 2010

> Dear users,
>  I think the pressure control in gromacs 4.0.7 may have some problems. First ,The pressure value >fluctuates widely ,even between -7984.377930 and 5920.053711 bar.Second,the average pressure >sometimes is much larger than what I have set,for example, I have set ref_p  = 1.0 , but the average is >actually over 7 bar. It is because I have not set properly , or something else?
> Zhongjin He

Hello Zhongjin:

The average pressure in gromacs is really somewhat larger, e.g. if you
request ref_p=1bar, you always get something close to P=1.3 bar. If
somebody can comment on this issue, it will be interesting. Anyway, I
think that the coupling in general is correct, since the simulated
densities are as they are expected.

As I suppose, the main reason is that pressure is not a nanoscopic
property whereas your MD system is nanosized. I would advice you to
gradually enlarge the system and monitor the pressure. It should give
you some answers anyway.

The average of  7 bar if one requests 1 bar, is weird. Look at the
simulation time and the system size firstly.


Dr. Vitaly Chaban
Associate Researcher

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