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

Hannes Loeffler 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
> post-hoc.

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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