Re: ABF tutorial; updated FEP tutorial

From: Lei Shi (
Date: Thu Mar 20 2008 - 17:38:40 CDT

Hi, Jerome

On page 15 of the alchemical FEP tutorial,
"A periodic cell length of L = 29.1A yields a size-dependence correction of
−16.2 kcal/mol"
Can you show more details on how you get the "-16.2" value?

In addition, in Table 4 of Grossfield et. al. (JACS 2003
125:15671-82), there are a few values for Na solvation, is the "-91.0" there
for charmm27 comparable to your -94 or -110.2?


On Thu, Mar 20, 2008 at 4:55 PM, Jerome Henin <>

> Dear NAMD users,
> We are happy to announce a brand-new ABF tutorial - an occasion for
> the curious among you to get acquainted with the method, working on
> three simple cases that should let you have the fun without too much
> of the pain:
> The alchemical FEP tutorial has also been updated, including a new
> exercise about a purely electrostatic perturbation, to see a slightly
> different kind of physics at play:
> Check them out, and let us know if you have comments!
> Jerome Henin and Chris Chipot

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