[gmx-developers] Gromacs 3.3.4 PME energies keep changing with longer cutoffs
dommert at icp.uni-stuttgart.de
Thu Feb 18 11:04:36 CET 2010
Berk is completely right, so I would also suggest to compare forces instead of energies. An appropriate set of parameters is hard to determine, since you have a bunch of possiblities to obtain an accurate force calculation. I would suggest to calculate reference forces with the help of a standard Ewald sum that has a large cutoff and a splitting parameter of about 3 and K=128. Since you can not input beta directly some small hacking of the code is necessary. src/gmxlib/ewald_util.c contains the routine calc_ewaldcoeff. Just change it that you input a negative value for ewald_rtol that is then given out as the corresponding positive beta. So something like this at the beginning of the routine:
Then you can input the splitting parameter directly and play around with it.
On 18.02.2010, at 08:12, hess at sbc.su.se wrote:
> 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.
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Institute for Computational Physics
EMail: dommert at icp.uni-stuttgart.de
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