Atomically detailed simulations of helix formation with the stochastic difference equation.
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.
Department of Computer Science, Cornell University, Ithaca, New York 14850, USA.
Alfredo E
AE
Cárdenas
Ron
R
Elber
D000465:Algorithms; D003198:Computer Simulation; D004151:Dipeptides / Q000737:chemistry*; D004735:Energy Transfer; D008958:Models, Molecular; D015233:Models, Statistical; D009038:Motion; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D013269:Stochastic Processes
D004151:Dipeptides; D011506:Proteins; C034792:valylvaline