MD without SHAKE

From: Dayle Smith <smithd_at_U.Arizona.EDU>
Date: Mon 26 Feb 2001 18:06:33 -0700 (MST)

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
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