> For a good evaluation of vdW energy, do I have to make an average of
> all the vdwaals values of all the outputs in a production MD run, or
> just the last value of the last step? What do you recommend?
The interaction between ligand/DNA will be combined with intra-DNA
and intra-ligand vdw (same for electrostatics; also water interactions) -
I don't think anyone uses the total vdw for anything more than analyzing
how well equilibrated the system is.
Ideally you might want the DNA/ligand interaction energy over time.
This is complicated by the fact that actual energy in solvent is
calculated for infinite periodicity with Ewald sum. There was a
program called Anal that calculated first-order energy between
groups of atoms; if this is still available, it might meet your
need adequately.
Bill
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Received on Thu Apr 22 2010 - 10:00:03 PDT
