Stochastic Path Approach to Compute Atomically Detailed Trajectories:  Application to the Folding of C Peptide

Abstract

A novel method to compute long-time molecular dynamics trajectories is employed to study the folding kinetics of C peptide. The computational method makes it possible to use a time step larger by orders of magnitude compared to widely used molecular dynamics integrators. Rather than solving the trajectory in small time steps, the whole trajectory is optimized. The algorithm filters high-frequency modes that are modeled as Gaussian noise. The assumption of “Gaussian noise” is tested numerically in two cases and found to be adequate. In all, 31 trajectories of C peptide that folds into a helix in explicit solvent (TIP3P water molecules) are computed. The time step is 500 ps. The folding pathways and the early formation of structure are discussed. Comparisons to a 2-ns trajectory calculated with the usual molecular dynamics approach and to available experimental data are made.