[gmx-developers] Gromacs 3.3.4 PME energies keep changing with longer cutoffs

hess at sbc.su.se hess at sbc.su.se
Thu Feb 18 08:12:45 CET 2010


I would like to add to this discussion that the energy is probably
not the best quantity to look at. If errors in pair energies
are uncorrelated (which they are not really), the error in the total
energy will scale as the square root of the number of particles
and the relative error will therefore seemingly decrease with system
size. You should look at the error in the forces.
But in both cases there is still the issue that you probably
don't now what value of the error is acceptable.


> I now observe you're using 3.3.4. The general nature of my comments
> still applies, but your npme is the number of cpus. You'll get
> substantially better performance from 4.0.7 unless you need 3.3.4 for
> some kind of scientific continuity.
> Mark
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