Re: How to use ParseFEP plugin to carry out FEP analysis for several forward and backward *.fepout files when lambda is from 0 to 1

From: Chris Chipot (
Date: Sun May 05 2013 - 02:44:48 CDT


if it bothers you to have multiple fepout files for your forward and your
backward transformations, why don't you make a single file for each
transformation by concatenating the different pieces? That would be
the easiest.

Chris Chipot

On 5/4/13 9:23 AM, dbaogen wrote:
> Dear all,
> I have met a problem to deal with free energy calculation using
> ParseFEP plugin. The forward analysis of FEP calculation using NAMD
> software is divided into several parts when lambda value is changed
> from 0 to 1. For example, lambda: 0~0.2, 0.2~0.4,.... Using the same
> strategy, backward analysis is also done.
> Under this condition, if I want to use ParseFEP plugin to calculate
> relative free energy, what should I do to deal with several forward
> and backward *.fepout files. Would you like to give me some help.
> Thanks for any suggestions.
> Best wishes
> Duan Baogen
> Beijing computational science research center

Chris Chipot, Ph.D.                    
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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