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

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