From: Chris Chipot (chipot_at_ks.uiuc.edu)
Date: Wed Jan 21 2009 - 17:32:52 CST
the free-energy change provided by NAMD in the fepout file is updated
on the fly at each time step of your simulation. To match the value
supplied by NAMD, your post-processing, therefore, ought to include
*all* potential energy differences, i.e. by setting fepOutFreq to 1.
This is correct: Removal of the singularity with the soft-core
interaction implicitly suppresses the linear λ-dependence of the
potential energy function. In double-wide sampling simulations,
since at any given value of λ, NAMD estimates the forward free-energy
change from λ to λ+δλ and the backward free-energy change from λ to
λ-δλ, it is not clear to me why two different values of λ should be
used. Remember that the backward simulation is expected to be the
mirror image of the forward. If electrostatic interactions are turned
on at λ in the forward run, it means that they are turned off at the
same value of λ in the backward run. Note that the CVS version will
include soon the double-wide sampling algorithm.
Sébastien Légaré a écrit :
> Dear NAMD users and developpers,
> I have a theoretical question about the use of separation-shifted vdw in FEP,
> now available in the cvs code. As stated in the FEP tutorial, linear scaling
> of the potential allows double-wide calculation with a single transformation.
> The only way I found to do this precisely is to post-process with all computed
> dE, so I need to set fepOutFreq to 1. Is there an other way?
> My main question is: Since it is not a linear scaling, shouldn't it be
> necessary to provide a second comparison lambda in order to do double-wide
> calculations with separation-shifted vdw?
> Thanks for this implementation, it will be very useful.
> Sébastien Légaré
> Ph. D. Student
> Laval University
> Quebec, Canada, G1V 0A6
> 418-656-2131 #11577
Chris Chipot, Ph.D.
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign
405 North Mathews Phone: (217) 244-5711
Urbana, Illinois 61801 Fax: (217) 244-6078
To sin by silence when we should protest makes cowards out of men
Ella Wheeler Wilcox
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