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

[Michael Shirts]

Yep, that's what I generally do.  Almost all alchemical changes involve a
difference in two calculations (since the alchemical change itself is
unphysical).  Even one-calculation solvation free energy calculations are
actually calculating the difference in free energy from liquid to vapor
state.

On Tue, May 19, 2015 at 11:58 AM, Hannes Loeffler <
Hannes.Loeffler at stfc.ac.uk> wrote:

> 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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