[gmx-users] couple-moltype in FEP

[Hannes Loeffler]

On Tue, 12 Jul 2016 12:44:10 +0200
Alexander Alexander <alexanderwien2k at gmail.com> wrote:

> 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.

I think it should be fairly straightforward to define two new
moleculetyps with a new name each, rename and reorder the coordinate
file accordingly and make the few changes in the [molecules] section.


> 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?

You would need to read the paper.  Since this is a decoupling exercise
my guess would be that the restraints are relative to the Ti surface.