[gmx-users] couple-moltype in FEP

[Hannes Loeffler]

On Tue, 12 Jul 2016 10:29:04 +0100
Hannes Loeffler <Hannes.Loeffler at stfc.ac.uk> wrote:

> On Tue, 12 Jul 2016 10:16:24 +0200
> Alexander Alexander <alexanderwien2k at gmail.com> wrote:
> 
> > Hi,
> > Thanks for your response.
> > I want to calculate the binding free energy of a single amino acid
> > to a solid surface in aqueous solution by FEP, alchemical
> > transformation, where perturbations applying on different species in
> > ordered steps. For instance: Step.1 applying harmonic restraints  to
> > the O and H of the amino acid. Step 2. Charges removal from the
> > amino acid and two water molecules and an Ion, happen.
> 
> I think the key figure here is actually Fig. 1.  What that paper
> attempts to do is to replace a molecule on a surface with two water
> molecules through a decoupling scheme.  I guess with Gromacs you would
> have to manipulate the topology files to some extent because the
> decharging and recharging steps involve different species (the sodium
> ion is there only to offset any changes in total charge).
> couple-lamnda0/1 may be helpful for some steps.  There are also both
> insertions and deletions so I think step 3 must be split into two vdW
> (deletion) steps.

Thinking about step 3 you could probably also do it as a relative
transformation i.e. omit couple-moltype and work with explicit A and B
columns.