[gmx-users] couple-moltype in FEP

[Alexander Alexander]

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.
.
.
.
Please have a look at FIG.6 of this paper in which AMBER has been used
(http://pubs.acs.org/doi/full/10.1021/ct400487e)

Actually, I was thinking about your first suggestion, but with two topology
files and two mdp files, however, using the last .gro file of the first
step as input for the second step. And also appending the result of the
second step to the results of the first step.

Best regards,
Alex

On Tue, Jul 12, 2016 at 9:47 AM, Hannes Loeffler <Hannes.Loeffler at stfc.ac.uk
> wrote:

> 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?
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>