[gmx-users] FEP and soft-core potentials
G.N.Patargias at leeds.ac.uk
Tue Jul 24 18:42:58 CEST 2007
Thanks once more for your reply David.
Do you know by any chance if we can get the dVpot/dlambda
for one of the default group of atoms (e.g. protein) rather than
for the whole system?
Dr. George Patargias
Polymer IRC Group
University of Leeds
Leeds, LS2 9JT, UK
From: gmx-users-bounces at gromacs.org on behalf of David Mobley
Sent: Tue 7/24/2007 5:00 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] FEP and soft-core potentials
Right. In fact, usually you would lose efficiency by using soft core
potentials for an electrostatic transformation over doing it without
soft core. The purpose of soft core is just to fix the problem with
disappearing/inserting atoms which have 1/r^12 repulsion.
On 7/24/07, Georgios Patargias <G.N.Patargias at leeds.ac.uk> wrote:
> Just a quick question about Free Energy Pertubation simulations. Do I understand
> correctly that if the only thing that changes from State A to B is the partial charge
> of a single atom, then I don't need the soft core potentials?
> Best wishes
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