[gmx-users] Re: Pressure control in GROMACS 4.0.7
David van der Spoel
spoel at xray.bmc.uu.se
Sat Jul 10 13:17:57 CEST 2010
On 2010-07-10 12.40, Vitaly Chaban wrote:
> Dear Professor van der Spoel:
> Don't you have an idea why the average value of pressure appears to be
> (always?) slightly larger and (never?) smaller than requested one? I
> did not collect the statistics systematically but I often mentioned
> this curious fact.
My guess is that it is just coincidence. In fact I published a table of
pressures with standard deviation in JCP 108 (1998) p. 10220 where some
pressures are rounded to 0, most to 1 and some larger than 1. This is
also my source for the fluctuations of 600 bar for a 216 molecule box.
These were with RF and Cut-off, it might be slightly different for PME.
>> 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.
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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