Regenerations of Initial Velocities in Parallel Cascade Selection Molecular Dynamics (PaCS-MD) Enhance the Conformational Transitions of Proteins

Abstract

Parallel cascade selection molecular dynamics (PaCS-MD) is a rare event sampling method. PaCS-MD repeats cycles of resampling from important initial structures based on short-time MD simulations. When restarting the short-time MD simulations, regenerations of the initial velocities play an essential role in creating perturbations to promote conformational transitions. Therefore, we addressed the conformational sampling efficiencies of PaCS-MDs with and without the regenerations of initial velocities by modeling the folding of a mini-protein (Chignolin) in explicit water. In the present letter, we confirmed that the regenerations of initial velocities increased the conformational sampling efficiency of PaCS-MD.