[gmx-developers] More about the Ekin issue.
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
> 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.
> This mail sent through IMP: http://horde.org/imp/
> gmx-developers mailing list
> gmx-developers at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-developers-request at gromacs.org.
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
More information about the gromacs.org_gmx-developers