Enhancing systematic motion in molecular dynamics simulation

Abstract

The self-guided molecular dynamics (SGMD) simulation method has been developed to accelerate the conformational search process. This method is based upon the understanding that slow systematic motion limits the conformational search efficiency in molecular dynamics (MD) simulation. The concepts of the local conformational space, local free energy and local free-energy force, are introduced to characterize the systematic motion of a system. The local free-energy forces are introduced into the equation of motion as guiding forces to accelerate the systematic motion in a conformational search.