[gmx-users] yet another question on pressure fluctuations

David van der Spoel spoel at xray.bmc.uu.se
Sun Oct 29 22:57:33 CET 2006

Daniel Cheong wrote:
> Dear all,
> I am relatively new to Gromacs, having only used it for a month or so.  I
> have read through the mailing list and have seen several question regarding
> the large fluctuations in pressure observed during the simulations.  This
> appears to be normal and expected in small system sizes and microscopic
> systems, so I guess there's not too much I can do about that.  But my
> question is this: if the pressure exhibits such wild fluctuations, does the
> imposed or calculated pressure mean anything?  In other words, say I am
> trying to calculate the interfacial tension of an oil-water interface at 1
> bar, and I run an NPT simulation, will the calculated surface tension mean
> anything when the pressure fluctuations are about 200bars?  Will the imposed
> pressure of 1 bar even mean anything at all?  Thanks for any help and
> insights you can give.
Yes it is fine. You can compute the surface tension as a function of 
time (as a matter of of fact mdrun does it for you). Then you should do 
averaging and a standard error analysis. A simple possibility is to use 
the -ee flag on g_analyze
g_analyze -f surftens.xvg -ee
Please do read the accompanying paper to understand the background of 
this matter.

Earlier tests show that mdrun is well behaved, i.e. errors fall as the 
sqrt of the number of particles and roughly as the square root of time 
too (but not fluctuations!).

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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