[dnd] MD aspect of DND

[Justin Bradford]

> >  The dnd version 0.5.1 ,which is in CVS, has a bug of the calculation of
> > potential energy. But I use water box in which there are 125 tip3
> > molecules to test the molecular dynamics simulation in DND.
> > 
> 
> I'm curious about the algorithm and force field being used for DND.  I'm
> familiar with CHARMm and AMBER, which are both commercial.  Many of the most
> common MD programs in fact have a common "ancestry".  Where does DND fit in? 
> Are there any journal references to check out?

I haven't had the chance to dig through the code for DND yet, but I was
wondering the same thing. Do you use a fast multipole algorithm or
something related? They are nearly O(N) for the number of molecules in the
simulation.  Furthermore, a group at Duke has done a lot of research on
the topic and come up with a distributable parallel version. Both SIgMA
and NAMD use  their library. I'll check the license on it, but regardless,
the algorithm is well documented and it would be possible to reimplement.

This is the homepage for the Duke library.
http://www.ee.duke.edu/Research/SciComp/Docs/Dpmta/


Justin