AMBER Archive (2006)

Subject: AMBER: Calculate interaction energy between small organic molecules

From: Björn C-G. Karlsson (
Date: Mon Aug 21 2006 - 01:37:24 CDT


I have been using Amber 8 to simulate the interactions between small organic
molecules in organic solvents such as chloroform and acetonitrile (explicit
solvent) using NVT and NPT molecular dynamic simulations.

Now my question is: I know that it is possible to extract energy information
from a simulation such as Etot, Epot and Ektot using a script, but is it
possible to calculate the non-bonded interactions for single molecules
during a simulation plotting these values and so to speak get a rough
measurement on the binding energy when the molecule interacts with another
molecules and experiences a decrease in Epot?

I have seen that something like this has been published before however using
the MD software GROMACS (Li, X-Y.; Eriksson, L. A. Molecular Dynamics Study
of Lignin Constituents in Water (2005). 59, 253-262.) However, can this be
performed using the Amber 8 software and how do I do it?





Björn C-G. Karlsson

PhD Student in Organic Chemistry

Department of Chemistry and Biomedical Sciences

University of Kalmar

SE-391 82, Kalmar, Sweden

Tel: +46 (0)480-44 62 80

Mobile: +46 (0)70-6150 444



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