tsjerkw at gmail.com
Fri Jan 5 16:14:49 CET 2007
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.
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
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