Classical Simulation Methods

The potential energy surfaces of biological, polymer, and other systems of interest to nanotechnology applications are usually written as sums of interactions between chemically bonded atoms (stretch, bend, torsion, improper torsion, and so on) and non-bonded interactions. MD and other molecular simulation methods require first and sometimes second derivatives of potential energy terms. A potential energy term V(<p),\ where <t> is an internal coordinate, has the following first and second derivatives:

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