Electrostatic Potential Problems, WRT Minimizations

From: Rajan Vatassery (rajan_at_umn.edu)
Date: Thu Oct 21 2010 - 21:34:23 CDT

Dear List,
        I'm trying to minimize the structures of molecules as they are
constrained to the surface of a sphere. The problem that I am having is
that the molecules have a small charge that seems to be attracting
together. Normally this is not a problem, but in my minimization, the
negative charges are attracting together. I have included all the
relevant files at:
http://www.tc.umn.edu/~rajan/NAMD-l.html , and if you open the PDB
output file that I received, you'll see that the negative charges are
very close to each other.

        Also on the above website, I have included a matlab screenshot of what
I consider to be the relevant distances and electrostatic PE
contributions as pertains to an arbitrarily selected molecule. My
calculation seems to show that this close contact of the negative
charges should not be at a lower energy than the situation in which this
molecule is infinitely far away from the other molecules. I have also
included graphs of the VDW, Electrostatic and Total energies. I have cut
the tops off the VDW and total energies since there were some unphysical
contacts at the beginning of the minimization.

        Again, I am completely lost and I'm sure I just overlooked something,
so I hope that an extra set of eyes will help me solve this problem.
Thanks in advance,


PS please let me know if I should post anything else and I will do so

Rajan Vatassery
Department of Chemistry
University of Minnesota

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