[gmx-users] Re : tau_p

chetana baliga baliga.chetana at gmail.com
Mon Jan 8 14:11:44 CET 2007

Thank you, Sir. I read from the mailing list archives, that it is not
just the value of tau_p but the ratio of compressibility to tau_p
which matters in Berendsen presure coupling.  I am using SPC water as
the solvent. Is there any ideal value for compressibility to be used
for SPC water? i have used a value of 4.5e-5, and a tau_p of 1.0 ps,
and my pressure coupling is isotropic.  Should the tau_p value be
increased or decreased to get a pressure average closer to ref_p? [I
am getting an average of 4.6 bar, while my ref_p is 1.0 bar, after a
time period of 6 ns of md simulation].




>Well, tau_p rather controls how the pressure fluctuates around the
>average..., ref_p is your attempt to control the average (if your
>system is set up properly).



On 1/5/07, Mark Abraham <mark.abraham at anu.edu.au> wrote:
> > Dear all,
> > I am running md simulations on a decapeptide, using pressure coupling
> > [npt].
> > My box is octahedral and box dimensions are set at peptide length plus
> > twice
> > the cut-off as recommended. I have set tau_p to be 1.0 ps. After 1 ns ,
> > the
> > average pressure had come down to 2.6 bar, though fluctuations were quite
> > high. [Standard deviation 150.8 ] But after 6ns, the pressure has risen
> > again to 4.6 bar. Can you please advise me on this?
> What was your equilibration regime? Over what length of time are you
> calculating these average pressures?
> > Also, can you please
> > tell me if there is any correlation between pressure average and tau_p
> > values?
> Yes, there will be for a properly set-up system.
> Mark

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