[gmx-users] tau_p
Oliver Beckstein
oliver at biop.ox.ac.uk
Wed Dec 17 16:43:01 CET 2003
> > I done MD for my sistem ( CL- NA+ 330Water)
> >at P=cte.
> >; Isotropic pressure coupling is on
> >Pcoupl = berendsen
> >Pcoupltype = isotropic
> >tau_p = 1.0
> >compressibility = 4.5e-5
> >ref_p = 1.0
> >The presure is really bad, very bad (average -0.5 bar, after 100ps)
> >I change tau_p= 0.5, then I obtain less fluctuacions.What is the
> >right value(s) of tau_p?.
> >
> 100 ps to average the pressure is really too small. Try at least 1 ns
> ... should be better.
For your information, after 100ns of 1M NaCl (39 Na+, 39 Cl-, 2102 water)
I obtain
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Pres-ZZ (bar) 1.05953 347.934 347.932 4.24344e-05
4.22362
(I did not use isotropic P-coupling but fixed x and y to be able to
compare to other simulations which required semiisotropic P-coupl; for
bulk I'd normally also do isotropic as you did. I used SPC water and the
ion params from ffG43a1; PME electrostatics, tau_p = 1.0, same ref and
compressibility as above).
Thus after sufficiently long time the average converegs on the preset
value, more or less. The fluctuations are still huge, of course.
Oliver
--
Oliver Beckstein * oliver at biop.ox.ac.uk
http://sansom.biop.ox.ac.uk/oliver/
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