From: Sundaramoorthy, Munirathinam (m.sundaramoorthy_at_Vanderbilt.Edu)
Date: Tue Dec 30 2003 - 12:21:59 CST
NAMD supposedly expresses energy in kcal/mol units. But the numbers for
the values of energy in minimizations are generally few orders of
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
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
-50,000. Is -50,000 kcal/mol really delta G for this interaction? How do
interprete this result?
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