From: "Alexey Shaytan" <[EMAIL PROTECTED]>
Reply-To: [EMAIL PROTECTED],Discussion list for GROMACS users
<gmx-users@gromacs.org>
To: gmx-users@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.
Indeed.
I have only implemented this in the development version.
Berk.
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