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

David Mobley dmobley at gmail.com
Thu Jan 4 18:36:40 CET 2007


>  From your mail it seems as if your bonded interactions do not influence
> dvdl,
> then you can also not calculate bonded interactions, this also makes
> sure the bonded
> forces are not double counted.

I am not sure what you mean by the bonded interactions not influencing
dvdl? And actually, what I am interested in here is the total
potential energy, not dvdl: I want the correct total potential energy
for the timestep I am at, at the lambda value of interest. I don't
want to have to assume I am not changing any bonds as a function of
lambda: This isn't something I want to use just for one particular
application; rather, a bunch of folks will be doing free energy
calculations with GROMACS, and will switch to using this approach for
calculating the free energy differences, so it needs to be fully

> The only thing I am not sure of is if the virial is not overwritten.
> For efficiency you also want to call only the free-energy energy loops
> in nonbonded.c
> for the other lambda values.

What do you think of the approach Erik discussed in his mail?


> Berk.
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