toma0052 wrote:
Hello,
I am simulating a lipid bilayer system, and am having some trouble
understanding the pressure output. When I run a simulation, even when I do
not add any perturbations or fix any atoms, the pressure oscillations are
quite large. The temperature coupling seems fine. After about 1ps, the
system is near the reference temperature, and the oscillations are only about
1 or 2 degrees. So, I expected something, roughly, similar with the
pressure. For the pressure, however, my reference pressure is 1.0 bar, but
the pressure in the system after a few picoseconds seems to range from -400
to 400 bar. Is this normal? Do I just need to wait longer? Does this mean
that I did not run the energy minimization long enough and there are some
high forces? Is there something else that I am doing wrong?
In my mdp file, the pressure coupling looks like:
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p= 0.5
compressibility = 4e-5
ref_p= 1.0
I have also tried Parrinello-Rahman pressure coupling with the same result.
Thanks
Mike
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this is normal.
increase your system size to reduce the fluctuations. scales as sqrt(n) :(.
--
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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