mark.abraham at anu.edu.au
Fri Jan 5 15:39:39 CET 2007
> Dear all,
> I am running md simulations on a decapeptide, using pressure coupling
> My box is octahedral and box dimensions are set at peptide length plus
> the cut-off as recommended. I have set tau_p to be 1.0 ps. After 1 ns ,
> 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
Yes, there will be for a properly set-up system.
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