Re: FEP calculation is doing nothing

From: Chris Chipot (
Date: Tue Aug 10 2010 - 11:06:11 CDT


it all depends whether or not you are considering the perturbation of
intramolecular contributions or not, which NAMD allows you to do by
means of the *decoupling* keyword.

Chris Chipot

On 8/10/10 10:09 AM, sudipta wrote:
> Hi All,
> I want to calculate the free energy change for a process like
> ALANINE(g)------>DUMMY(g) in vacuum by Free energy perturbation method.
> DUMMY means nothing. So that I have set -1.0 in the beta column for all
> the atoms in my system of the .fep file. Unfortunately I have seen no
> energy difference between two successive lambda values. Can anybody
> please tell, why the energy difference between two lambda values is
> zero, when I run a FEP calculation in vacuum.
> Thanks and regards
> Sudipta


Chris Chipot, Ph.D.
on leave from Nancy Université, CNRS
Theoretical and Computational Biophysics Group
Beckman Institute
University of Illinois at Urbana-Champaign
405 North Mathews Phone: (217) 244-5711
Urbana, Illinois 61801 Fax: (217) 244-6078


The light shines in the darkness, and the darkness has not overcome it.
                                                               John 1:5.

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