From: Ramie (
Date: Fri Jun 14 2013 - 07:58:04 CDT

Hello everybody,

         I am using the ParseFEP plugin in VMD
(Extentions/Analysis/Analyze FEP Simulation) in windows to estimate
the error of an Alchemical Free Energy calculation performed using
NAMD only in the forward direction. I used the output file
forward.fepout produced by NAMD as an input to ParseFEP plugin
(Version 1.5) as "FEP output file". The temperature is set to 300.0
and everything else is unchecked, including FEP(backward) output file.
When I click on Run FEP parsing it runs fine with "All calculations
complete" at the end and a lots of values like A, sigma, epsilon,
delta-epsilon etc etc. are produced. Can you please help me identify
the error estimation of the free energy? The manual does not seem to
be helpful and it does not give any examples.

Thank you very much,

Be the Change You Wish to See in the World - Gandhi
Dr. Obaidur Rahaman
Institut de Biologie Physico-Chimique
Centre National de la Recherche Scientifique
75005 Paris, France
Tel: 06 61 21 36 53