binding energy

From: bora erdemli (
Date: Tue Dec 14 2004 - 07:38:05 CST

Dear Namd users;

I would like to calculate binding energy. I did three
simulations one of them was for dimer and the other
two were for individual monomers at the same
Is it correct to calculate binding energy as follows?

1)calculate the ensemble average of total energy of
dimer and two monomers

2)binding energy = Energy of dimer - energy of
monomer1 and energy of monomer2

or Is there any other more reasonable way of doing


Sabri Bora Erdemli
Koc University
Computational Science and Engineering
Research and Teaching Asistant
Koc Universitesi pk.218 34550
sariyer Istanbul/TURKEY
tel no: 02123381736

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