[gmx-users] couple-moltype in FEP

[Hannes Loeffler]

On Tue, 12 Jul 2016 07:35:00 +0100
Hannes Loeffler <Hannes.Loeffler at stfc.ac.uk> wrote:

> On Tue, 12 Jul 2016 01:56:42 +0200
> Alexander Alexander <alexanderwien2k at gmail.com> wrote:
> 
> > I was wondering that how I can have for example two different
> > "couple-moltype" in free energy part of my *.mdp file in FEP,
> > alchemical transformation? The reason for having two is to perturb
> > each of them differently in ordered steps.
> 
> You don't quite say what you are trying to do but you can always work
> with more than one topology file.

I got that one wrong.  When you use couple-moltype you obviously want
to make a whole molecule disappear without touching the topology.
Can't you just do two runs with different couple-moltype?