[gmx-users] Fwd: Bad performance in free energy calulations

[Michael Shirts]

>
> somewhat off-topic but I wonder why in your free energy protocol you
> only vary the vdW and electrostatic lambdas.  What about the others?
> Your mutation also transforms bonded terms and masses.
>


Minor point - if you are taking the difference between two mutations (say,
with and without a ligand), then it's better to leave the masses untouched
-- any contribution will cancel.  There are some weird issues with changing
masses in the constraint terms and their contribution to the free energies
that need to be accounted for post-hoc.