From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Tue Dec 30 2003 - 13:53:17 CST
Hello Sundar,
Interaction energies are not the same as free energy (delta G)
DeltaG also includes the temperature and system entropy.
Unless you know of a way to sum through all entropic states the energy
from NAMD and free energies from experiment will never be same.
Brian
On Tue, 30 Dec 2003, Sundaramoorthy, Munirathinam wrote:
>
> NAMD supposedly expresses energy in kcal/mol units. But the numbers for
> the values of energy in minimizations are generally few orders of
> magnitude
> different compared to experimentally measured values.
>
> For example, I have calculated the energy of interaction between two
> protein chains and also, the energy was calculated experimentally.
> The crystal structure of the dimer is available. So I minimized the
> dimer
> structure (AB) and minimized the monomers (A and B) separately. All were
> done in appropriate spheres of solvent. The interaction energy was
> calculated as (EtotalA + EtotalB) - EtotalAB, which turns out to be
> circa
> -50,000. Is -50,000 kcal/mol really delta G for this interaction? How do
> I
> interprete this result?
>
> Thanks
> Sundar
>
>
-- ***************************************************************** **Brian Bennion, Ph.D. ** **Computational and Systems Biology Division ** **Biology and Biotechnology Research Program ** **Lawrence Livermore National Laboratory ** **P.O. Box 808, L-448 bennion1_at_llnl.gov ** **7000 East Avenue phone: (925) 422-5722 ** **Livermore, CA 94550 fax: (925) 424-6605 ** *****************************************************************
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