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].
Regards,
Chetana.
Hi,
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).
Cheers,
Tsjerk
On 1/5/07, Mark Abraham <[EMAIL PROTECTED]> 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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