Re: Sampling schemes with FEP

From: Chris Chipot (chipot_at_ks.uiuc.edu)
Date: Thu Oct 20 2011 - 09:16:34 CDT

George,

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.

Cheers,

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 (http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/13813.html)
> 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
                             E-mail: chipot_at_ks.uiuc.edu
                                     Christophe.Chipot_at_edam.uhp-nancy.fr
                             Web:    http://www.ks.uiuc.edu/~chipot
                                     http://www.edam.uhp-nancy.fr
The light shines in the darkness, and the darkness has not overcome it.
                                                               John 1:5.
_______________________________________________________________________

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:24:29 CST