combine PMF/dual FEP -> correct free energies?

From: Sebastian Stolzenberg (
Date: Thu Dec 11 2008 - 19:09:28 CST

Dear Jerome, Dear All,

I need to do some free energy calculations with restraints. To get a
correct free energy value, I decided to separate my calculations into
three parts:

a) gradually add a few positional restraints (PMF module with 'slow
growth - up')
b) dual-topology transformation (alchemical FEP module)
c) gradually release positional restraints (PMF module with 'slow growth
- down')

Sum of all 3 free energy differences=total free energy difference
To maintain the final restraints from a) in b), I will simply impose a
tclSCript with exactly the same force constants and equilibrium distances.

Does this combination of PMF/dual FEP work in practice to obtain
reasonable free energies? If no, what other options should I consider

Thank you,

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