[gmx-users] FEP and soft-core potentials

[Georgios Patargias]

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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