double-wide sampling with soft-core

From: Sébastien Légaré (Sebastien.Legare_at_rsvs.ulaval.ca)
Date: Tue Jan 20 2009 - 14:27:32 CST

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

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