From: Chris Chipot (chipot_at_ks.uiuc.edu)
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.
On 10/20/11 8:13 AM, Patargias, George wrote:
> 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.
-- _______________________________________________________________________ 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. _______________________________________________________________________
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