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?
Thanks,
Bob
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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.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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