[AMBER] van der Waals energy component calculation

From: Dennis Stauffer <dstauffe.lakeheadu.ca>
Date: Tue, 19 Nov 2013 17:36:52 -0500

To whom it may concern,

We are performing molecular dynamics simulations of amino acids on
graphene and graphene oxide surfaces in water using the YASARA
software package and the Amber 03 force field. As part of our analysis
of the interaction energy between the amino acid and the surface, we
examine the contributions of the six energy components (bond, angle,
dihedral, planarity, coulomb, van der Waal) to the total interaction

Specifically, we are trying to determine how the amber 03 force field
calculates the van der Waal interaction energy between two atoms. In
the force field parameter file, we found values for the van der Waals
radius and the potential well depth for individual atoms. We would
like to know how the van der Waals interaction energy between two
atoms is calculated from these values.

The amber 03 manual cites the paper "Charge-dependent model for
many-body polarization, exchange, and dispersion interactions in
hybrid quantum mechanical/molecular
mechanical calculations," where, for the potential well depth, the
two-body parameters are determined from the one-body parameters by
adding two values for the individual atoms and dividing by 2. We would
like to know if this is how the van der Walls interaction energy is
calculated by the amber 03 force field or if another method is used.

Thank you in advance for your time.

Dennis Stauffer
Thunder Bay Regional Research Institute

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Received on Tue Nov 19 2013 - 15:00:03 PST
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