free energy perturbation

Date: Wed Jan 05 2011 - 02:07:57 CST

Hi, All:

I have a question about on comment in the FEP tutorial (Page 14),
which I quote as following:

" Since a soft-core potential [12, 13] has been introduced to avoid
the so-called “end-point catastrophes”, the potential energy no longer
varies linearly with the coupling parameter . It is, therefore,
necessary that the reverse transformation be carried out explicitly to
access G+!, as is proposed in the above NAMD scripts."

I do not fully understand the logic here. Why the reverse
transformation has to be carried out to access the dG in nonlinear
case? One should be able to calculate the energy difference, which is
needed to calculate dG, in either case.

Any input is greatly appreciated.


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