Simulation of conformational transitions by the restricted perturbation–targeted molecular dynamics method

Abstract

A method for the simulation of conformational transitions is presented. The method, based on targeted molecular dynamics (TMD), limits the conformational change at each molecular dynamics step to a fixed size, that minimizes the root mean square deviation from the target. The method is more efficient than standard TMD and yields lower energy pathways, but, like the TMD method, requires only a single molecular dynamics simulation. Test calculations and comparisons with standard TMD calculations for the alanine dipeptide with the analytic continuum electrostatics implicit solvent model are presented.