Re: alchemify FEP

From: Jérôme Hénin (
Date: Thu Feb 17 2005 - 15:04:18 CST

Hi Wei,

Derivation of the basic FEP expression shows that the kinetic contribution
cancels out.

Bonded terms are another problem. The FEP code in NAMD uses the (pretty
common) assumption that their contribution is negligible.
In the dual topology approach, the only bonded terms that would contribute to
the free energy are those involving perturbed and non-perturbed atoms. In
some systems, there will be no such terms (namely, when perturbing an entire
Although I am sure one can imagine particular cases when this approximation
make some small difference, but since the good use of alchemical FEP involves
taking differences between free energy variations inside a thermodynamic
cycle, most of this contribution is expected to vanish altogether.

A good reference on that would be:
S. Boresch and M. Karplus.
The role of bonded terms in free energy simulations. 1. theoretical analysis.
J. Phys. Chem. A, 103:103-118, 1999.


Le jeudi 17 Février 2005 20:14, Wei Chen a écrit :
> Hi,all,
> I am using alchemify FEP in NAMD to calculate free energy difference before
> and after mutating a residue in a peptide chain. However, I found that only
> VDW and electrostatic energy are included in the calculation of free
> energy. Why we do not need care about kinetic energy, bond stretching, etc.
> Who have any ideas?
> Regards,
> Wei Chen
> --

Jérôme Hénin
Equipe de Dynamique des Assemblages Membranaires
Université Henri Poincaré / CNRS
Tel : (33) 3 83 68 43 95        Fax : (33) 3 83 68 43 71

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