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Molecular Model and Data Structures

Andrew Dalke dalke at acm.org
Sun Dec 3 19:23:40 EST 2000

john slimick wrote in message ...
>I am building my own notes for our data structures course --
>I don't think existing texts address real problems in the real world.
>If there are MM programmers reading, could you suggest a place to find
>information on the data structures used to represent molecules?

There's plenty of source code available to look at, and some
contain additional documentation about the data structures used.
You might want to take a look at:
  TINKER  (in Fortran) - http://dasher.wustl.edu/tinker/
  NAMD  (in C++) - http://www.ks.uiuc.edu/Research/namd/
  MMTK  (in Python/C) - http://dirac.cnrs-orleans.fr/programs/MMTK/
  MOLDY (in C) - http://www.earth.ox.ac.uk/~keith/moldy.html
  GROMACS (in C) - http://rugmd0.chem.rug.nl/~gmx/software.html

Some of these sites have additional links to other programs.

The data structures aren't all the complicated for the simple
case.  The complications come in with, say, distributing the
simulation across many processors or optimizing non-bonded/
electrostatics terms.

                    dalke at acm.org

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