On 2010-07-10 09.47, Vitaly Chaban wrote:
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.
fluctuations are proportional to 1/sqrt(natoms). The numbers Zhongjin
mentions are extreme, for a 216 water box *in equilibrium* you would get
1 +/- 500-600 bar. I suspect your sytem may be out of equilibrium or
very small. Whether the average is 1 or 5 does not make a difference if
the fluctuation are two orders of magnitude larger.
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.
Best.
--
Dr. Vitaly Chaban
Associate Researcher
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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