Re: Sampling schemes with FEP

From: Chris Chipot (
Date: Thu Oct 20 2011 - 09:16:34 CDT


this is for the most part spelled out in the Pohorille, A.; Jarzynski, C.;
Chipot, C. /J. Phys. Chem. B, /*2010*/, 114/, 10235-10253 paper.

In addition, feel free to use the VMD plugin ParseFEP, which has been
designed for the post-treatment of NAMD FEP outputs. It features the
SOS and BAR estimators and their respective variances.


Chris Chipot

On 10/20/11 8:13 AM, Patargias, George wrote:
> Hi
> I just wanted to ask what is the state-of-the-art FEP sampling strategy
> with NAMD.
> According to Dr. Chipot (
> one can use both SOS and BAR estimators with the later being more accurate.
> Is this indeed the case?
> Many thanks.
> George

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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