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Atomically Detailed Simulations of Helix Formation with the Stochastic Difference Equation

Department of Computer Science, Cornell University, Ithaca, New York 14850

Correspondence: Address reprint requests to Ron Elber, Dept. of Computer Science, Cornell University, Upson Hall 4130, Ithaca, NY 14850. Tel.: 607-255-7416; Fax: 607-255-4428; E-mail: ron{at}cs.cornell.edu.

An algorithm is described to compute approximate classical trajectories as a boundary value problem with an integration step in the arc length. High-frequency motions are filtered out when a large integration step is used, maintaining the stability of the algorithm. At the limit of high filtering (large steps), but still offering an accurate description of the continuous path, the trajectory approaches the steepest descent path (SDP). The steepest descent path is widely used as a reaction coordinate in chemical systems. At intermediate step sizes, some inertial motions remain, interpolating between reaction coordinates and exact classical trajectories. Numerical studies of spatial and energetic properties of meta-trajectories are carried out. Two systems are considered here: valine dipeptide and the folding of a small helical protein. Although thermodynamic properties of meta-trajectories are affected by the filtering, the ordering of events remains similar for substantial differences in trajectory resolution.