Hi!
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?
Cheers/Björn
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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
bjorn.karlsson.hik.se
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Received on Wed Aug 23 2006 - 06:07:07 PDT
