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MathGroup Archive 1998

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Molecular dynamics with Mathematica?




Greetings

For a little project I am working on it would be nice to do some
molecular dynamics simulations using Mathematica.  I recognize it's not
the "perfect" package for such an undertaking, but the students
involved are familiar with it, and particularly with using it for
visualization.

For just a few atoms it's easy enough to program it up in a style
mimicking procedural programming, Verlet algorithm say.  But once there
are more than 10 or so the performance becomes unsatisfactory. 
Obviously,one could use NDSolve, but that's definitely overkill for
this case, and the performance is again terrible.  Has anyone done
molecular dynamics simulations in Mathematica?  What programming
approach did you use?  I'd like to get "reasonable" performance with up
to, say, 200 atoms.

right now I'm leaning towards doing it all with C code and MathLink, but
would prefer a simpler solution if one is available.

Thanks in advance --- Tom


--
Dr. Thomas L. Marchioro II
Department of Chemistry
University of Washington
206-323-9599
http://borg.chem.washington.edu/~tlm




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