Looking for info on hamiltonians for proteins.

roussel at hg.uleth.ca roussel at hg.uleth.ca
Tue Aug 22 22:26:18 EST 1995


In article <41at64$fnr at news.missouri.edu>, dons at cs.missouri.edu (Don Steiger)
writes:
>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.

     This is a question without a tidy answer.  Do you intend to do a classical,
semi-classical or quantum-mechanical calculation?  At what level do you want
to model the molecule?  Do you want a full model in which (assuming a quantum
calculation in the Born-Oppenheimer approximation) the electronic and nuclear
wavefunctions are both computed?  Would you be happy with a semi-empirical
electronic potential?  Would it suffice, for your purposes, to study a protein
model rather than a real protein?
     Protein modeling (and molecular modeling in general) is a big field
in which a lot of different techniques have been tried, with varying degrees
of success.  On the other hand, efficient parallel methods are certainly
in the early stages of development so it's quite possible that your
contribution will prove valuable.  There's a book by Karplus
and Porter which might serve as a useful springboard for further study.
(I can't recall the title just now.)
     Good luck.

                                           Marc R. Roussel
                                           Department of Chemistry
                                           University of Lethbridge
                                           roussel at zarqon.uleth.ca




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