From: Michael Grabe (mgrabe_at_itsa.ucsf.edu)
Date: Fri Feb 18 2005 - 01:26:17 CST
All of the papers using this technique
neglect the kinetic terms in the hamiltonian.
you should read the early work by peter kollman.
On Thu, 17 Feb 2005, Wei Chen wrote:
> 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?
> Wei Chen
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