dynamics disaster

Carolyn A. Kanagy checak at CHEMIND2.GSU.EDU
Tue Jan 23 13:47:59 EST 1996

Just ran a first dynamics run on DNA duplex with drug.
Disastrous results.  Are there any general guidelines
for troubleshooting these runs?  The DNA-drug complex
was unsolvated; temperature ramped to 300K, 150 psec of
dynamics run with .002 psec timesteps.  No constraints
except covalent hydrogen bond lengths.  Output not even
a good helix.  I ran 50 steps of Powell minimization
before the dynamics and noticed at the end of this time
that my methylene protons were bonded to one another,
among other things.  And that was just for starters.
Using Amber force field with modifications.  Any general
words of wisdom on how to approach this monumental mess?

Carolyn Kanagy
GSU Chemistry

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