[gmx-users] FEP and soft-core potentials

David Mobley dmobley at gmail.com
Tue Jul 24 23:26:05 CEST 2007


You can't. (And it probably wouldn't be meaningful if you could,
since, for example, the change in the protein-protein interactions
depends on what the water and ligand are doing).

David

On 7/24/07, Georgios Patargias <G.N.Patargias at leeds.ac.uk> wrote:
> 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?
>
> Best wishes
> George
>
> Dr. George Patargias
> Polymer IRC Group
> University of Leeds
> Leeds, LS2 9JT, UK
>
>
>
> -----Original Message-----
> 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.
>
> David
>
>
> On 7/24/07, Georgios Patargias <G.N.Patargias at leeds.ac.uk> wrote:
> > Hello
> >
> > 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?
> >
> > Thanks.
> >
> > Best wishes
> > George
> >
> >
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