Good afternoon.
I integrated a program into AMBER which calculates the electron affinities
of the thymine bases from their Cartesian coordinates in the MD
trajectory. However, with SHAKE turned on my electron
affinities are too low because the hydrogen-containing bonds are not
allowed to stretch.
My question is, can I run MD for solvated DNA with SHAKE turned off? What
settings should I use to make sure the simulation runs smoothly?
Thanks for your help.
-Dayle Smith
University of Arizona
Department of Chemistry
Received on Mon Feb 26 2001 - 17:06:33 PST
