[gmx-developers] doing energy evaluations at alternate lambda values (i.e. for bennett acceptance ratio)

David Mobley dmobley at gmail.com
Thu Jan 4 18:30:21 CET 2007


> I do have to loop over the lambda values, but only in the free energy
> loop, and since that normally only accounts for 1-2% of runtime it's
> not a problem to do it every single step.

For some reason I originally thought that this would also involve
multiple calls to PME, but now I'm thinking that's not the case. Is
that right? Are you sure there's nothing else that would be a bigger
percentage of the total runtime? My thinking, again, was to add a
counter that would allow the extra evaluations just to be performed
every so often. I realize, as David points out, that the statistics
output to the .ene files include information on all of the snapshots,
but we typically don't use those anyway (because we want to do
autocorrelation analysis on the timeseries of potential energies or
some such, and because correlation times are typically comparable to
the frequency at which we write energies to the ene file, so the extra
data doesn't buy us anything), so it wouldn't cost us anything to give
up having the energies stored every step.


> Cheers,
> Erik
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