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.
-michael
On Thu, 17 Feb 2005, Wei Chen wrote:
> 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
>
> --
>
>
>
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