Re: MD of DNA

From: Michael G Cooney <chemgc_at_panther.Gsu.EDU>
Date: Thu 6 Dec 2001 16:05:14 -0500 (EST)

Yes, I do notice this in my MD simulations of DNA. It is probably related
to the force constants in the out-of-plane (improper) torsion terms of the
force field, but if one takes an average MD structure these deviations
should cancel out. Also, any MD structure probably needs to be
energy-minimized before further calculations, and this also should restore
base planarity.

Hope this helps.


Michael G. Cooney
Postdoctoral Associate
Dept. of Chemistry
Georgia State University
Atlanta, GA 30303

On Thu, 6 Dec 2001, Marcela Madrid wrote:

> I was wondering if those of you who have experience doing MD of DNA
> can tell me if it is normal for the bases to deviate slightly from
> planarity
> during the dynamics.
> thanks! Marcela
Received on Thu Dec 06 2001 - 13:05:14 PST
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