[gmx-users] problem using pairtypes 2, 3 for free-energy decoupling

Berk Hess gmx3 at hotmail.com
Wed Aug 9 14:05:05 CEST 2006

>From: "Alexey Shaytan" <shaytan at polly.phys.msu.ru>
>Reply-To: shaytan at polly.phys.msu.ru,Discussion list for GROMACS users 
><gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] problem using pairtypes 2, 3 for free-energy 
>decoupling Date: Mon, 31 Jul 2006 19:18:44 +0400 (MSD)
>Dear Michael, Berk, all
>I'm currently trying to use GROMACS for calculation of solvation free
>energies for small molecules in water and hexane.
>Searching through the mailing archives I found the following method
>to decouple solvent-solute interactions:
>Berk Hess Wed Mar 1 09:30:25 CET 2006 wrote:
> >The idea is that for the solute to be decoupled one would replace
> >the in its [ pairs ] section type 1 by type 2
> >and exclude all intramolecular non-bonded interactions and replace
> >add them again explicitly in a [ pairs ] section as type 3.
> >
>However, trying to realize this method in GROMACS 3.3.1 release I
>encountered a problem:
>it seems that in my case grompp or mdrun disregards the type of pair
>interaction, assuming it always to be 1. And the pair interactions ARE
>pertubed during the free energy calculation.

I have only implemented this in the development version.


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