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Protein Engineering, Vol. 14, No. 11, 825-828, November 2001
© 2001 Oxford University Press

COMMUNICATION

An alternative derivation of the equations of motion in torsion space for a branched linear chain

Christopher Bystroff

Department of Biology, RPI, Troy, NY 12180, USA. E-mail: bystrc{at}rpi.edu

Torsion space molecular dynamics may be more efficiently encoded if the global motions are separated from the internal motions. The equations of motion for single, non-cyclic chains are shown to be first order in the backbone angle parameters when the global frame of reference is ignored and second order otherwise. Adding a simple heuristic substitute for the global motions enables the encoding of dynamics for mixed constrained/unconstrained model systems.


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