I would like to create a new reaction coordinate for use in adaptively biased MD. The AMBER 11 manual states (footnote, p.122) that this is really simple. Are there any instructions for this?
Specifically, I want to create a function modeled after N_OF_BONDS in which the deviations from a standard bond angle are measured. For example several theta angles will be monitored in double-straned DNA.
Mike
Dr. Michael F. Bruist
Associate Professor of Biochemistry
Department of Chemistry & Biochemistry
Griffith Hall 147
University of the Sciences in Philadelphia
Philadelphia, PA 19104-4495
Phone (Office & Voice Mail): (215) 596-8530
Department Phone: -8839
Department Fax: -8543
E-mail: m.bruist .usp.edu
web page: http://tonga.usp.edu/bruist
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Received on Fri Aug 19 2011 - 17:00:04 PDT
