[gmx-users] couple-moltype in FEP

[Alexander Alexander]

Yes, Fig.6 comes from the different step in Fig.1. I think the easiest way
here is to have 6 different "topol-mdp" files corresponding to each step.
Although unlike the amino acid, defining the [ moleculetype ] for ion and a
limited number of water molecules out of thousand of water molecules in the
box would not be that easy.

The harmonic restrants have been applied in step 1 and 3, can you please
let me know what is the difference between them and also how I can apply
each of them in md files?

Thanks,
Regards,
Alex

On Tue, Jul 12, 2016 at 11:33 AM, Hannes Loeffler <
Hannes.Loeffler at stfc.ac.uk> wrote:

> 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.
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