An alternative derivation of the equations of motion in torsion space for a branched linear chain.
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.
Bystroff
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Department of Biology, RPI, Troy, NY 12180, USA. bystrc@rpi.edu
D008958:Models, Molecular; D008962:Models, Theoretical; D009068:Movement; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
D010455:Peptides; D011506:Proteins