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.
Sincerely,
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
