[gmx-developers] doing energy evaluations at alternate lambda values (i.e. for bennett acceptance ratio)
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
> 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?
> 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.
More information about the gromacs.org_gmx-developers