From: Chris Chipot (chipot_at_ks.uiuc.edu)
Date: Thu Jan 22 2009 - 12:23:55 CST
Floris,
> One minor point, there's an explicit alchDoubleWideSampling parameter documented, maybe this could be dropped and inferred from the use of both lambdaPlusDelta and MinusDelta?
alchDoubleWideSampling < Will an FEP alchemical transformation be
performed in the forward and the backward
directions concomitantly? >
Acceptable Values: on or off
Default Value: off
Description: Simultaneous alchemical transformations in the forward and
the backward directions constitute a straightforward route
towards the estimation of the error associated to the
corresponding free energy calculations through their
hysteresis. When set to on, this option will request the
concomitant evaluation of the ensemble averages over
configurations representative of state λ, going (i) from
to λ+δλ (controlled by keyword alchLambdaPlusDelta), and
(ii) from λ to λ-δλ (controlled by keyword
alchLambdaMinusDelta). Accessing from a single free energy
calculation the statistical information of both
transformations is particularly useful for data
post-processing, e.g.BAR and SOS, which have proven to
improve the accuracy of the free{energy estimates over
brute-force application of the FEP formula. It should be
emphasized, however, that forward and backward
transformations do not necessarily share the same
convergence properties, so that, over finite-length
simulations, free-energy differences will not be strictly
equal.
As you correctly pointed out yesterday, and though everyone probably
knew what was implied in the Jorgensen-Ravimohan λ+δλ notation, one
should really think in terms of differences between λ and λ2, which
subsumes different δλ's along the reaction path.
Chris
_______________________________________________________________________
Chris Chipot, Ph.D.
on leave from Nancy Université, CNRS
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
http://www.edam.uhp-nancy.fr
To sin by silence when we should protest makes cowards out of men
Ella Wheeler Wilcox
_______________________________________________________________________
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