[gmx-users] couple-moltype in FEP

[Alexander Alexander]

Concerning to the harmonic restraints, in step 1. is just something inside
the molecule (as said applying restraints to the H and O atoms in HCOO-)
but in step 3 is restraint between waters molecules and surface, but my
question is in general how I should apply the harmonic restraint? If it is
by the "restraint-lambdas"? should I use "posre.itp"? should I use pull
code?

Thanks
Regards,
Alex

On Tue, Jul 12, 2016 at 2:40 PM, Hannes Loeffler <Hannes.Loeffler at stfc.ac.uk
> wrote:

> 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.
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