Don Steiger wrote:
>
> In part the answer depends on what definition of integrable you use. However,
> it is not hard to come up with a Hamiltonian that is not integrable under any (
> reasonable ) definition of the word integrable. What I would like try to do is
> integrate the hamiltonian of some molecule using a symplectic numerical
> integrator running on several loosely coupled processors. My problem is that I
> have no idea what a hamiltonian for a real life molecule looks like.
>
>
Don,
Molecular dynamics simulations typically assume a fairly
simple form for the molecular hamiltonian. One of the following
references should be available in your library:
"Proteins: A Theoretical Perspective..." by Brooks, Karplus
and Pettitt, John Wiley & Sons
"Dynamics of Proteins and Nucleic Acids" by McCammon & Harvey
Cambridge University Press
Both of these give concise and clear presentations of the
energy equations usually used for macromolecules. References in either
volume will point you to relevant articles that will provide more
detail regarding parameter sets and other niceties.
Regards,
Randy
All opinions expressed here are mine, not my employer's
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