[gmx-users] Fwd: Bad performance in free energy calulations
Hannes.Loeffler at stfc.ac.uk
Tue May 19 17:58:23 CEST 2015
On Tue, 19 May 2015 11:37:11 -0400
Michael Shirts <mrshirts at gmail.com> wrote:
> > 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
So you suggest to leave the mass lambdas simply at their initial (or
final) value to be safe in case constraints are involved (and I am too
lazy to check)?
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