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

[Hannes Loeffler]

On Tue, 19 May 2015 12:03:41 -0400
Michael Shirts <mrshirts at gmail.com> wrote:

> 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.

This reminds me: there was recently a discussion around couple-moltype
on this list.  My understanding is that this can be used for "absolute"
free energies.  But what I really want to make sure is this: as far as
I can see in the code and I think the manual says that too is that when
couple-moltype is not set in the .mdp none of the other couple-
parameters have any effect should I set any of the to something.  Do I
get this right?

Many thanks for the answers,
Hannes.



> 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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