[gmx-users] Huge fluctuations for pressure coupling
David van der Spoel
spoel at xray.bmc.uu.se
Wed Apr 19 17:52:09 CEST 2006
Bob Johnson wrote:
> Hello everyone,
> I have a 20 base single stranded DNA with counterions that is hydrated with
> about 9000 water molecules. My pressure coupling input looks like this:
> pcoupl = Parrinello-Rahman
> pcoupltype = isotropic
> ref_p = 1.01
> compressibility = 4.5e-5
> tau_p = 1.0
> However, I get huge pressure fluctuations (RMS fluctuation of 1.71704e+02) and
> it seems that the coupling doesn't even enforce the correct pressure (average
> pressure of 1.68282e-01). I didn't see anyone in the mailing list that had a
> similar problem. Does anyone know what's going on?
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this is normal.
you fail to specify what length of simulation this is. given the
fluctuations the average pressure is spot-on. if you want ten times
lower fluctuations you need hundred times more atoms :)
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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