[gmx-developers] More about the Ekin issue.

David spoel at xray.bmc.uu.se
Thu Aug 11 19:05:03 CEST 2005

On Thu, 2005-08-11 at 18:50 +0200, hessb at mpip-mainz.mpg.de wrote:
> I think the whole NPT REMD issue (which is no longer
> related to the subject) is caused by the, probably,
> incorrect CVS implementation of David.
> I think the highly fluctuating, meaningless instantaneous
> pressure in the criterion should be replaced by the reference
> pressure, as one considers an constant NPT ensemble.
> Just like a constant T is used in the criterion.
> The pV term then only depends on the instananeous volume,
> which fluctations do have meaning.
> BTW I think there is also a factor 1/PRESFAC missing in the exchange criterion.
Any obvious bugs apart from that then?

I will replace the instantaneous pressure by the constant trace of the
reference pressure.
> Then there is still the barostat issue.
> 400 waters at 300K, p=1 bar for 10 ns give:
> Berendsen volume: 11.968 rmsd 0.089
> Parrinello-Rahman: 11.977 rmsd 0.150

This is not relevant but the derived volume fluctuations are of course.

> Berk.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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