Directionally negative friction: a method for enhanced sampling of rare event kinetics.
A method exploiting the properties of an artificial (nonphysical) Langevin dynamics with a negative frictional coefficient along a suitable manifold and positive friction in the perpendicular directions is presented for the enhanced calculation of time-correlation functions for rare event problems. Exact time-correlation functions that describe the kinetics of the transitions for the all-positive, physical system can be calculated by reweighting the generated trajectories according to stochastic path integral treatment involving a functional weight based on an Onsager-Machlup action functional. The method is tested on a prototypical multidimensional model system featuring the main elements of conformational space characteristic of complex condensed matter systems. Using the present method, accurate estimates of rate constants require at least three order of magnitudes fewer trajectories than regular Langevin dynamics. The method is particularly useful in calculating kinetic properties in the context of multidimensional energy landscapes that are characteristic of complex systems such as proteins and nucleic acids.
MacFadyen
James
J
Department of Chemistry, University of California, Irvine, CA 92697, USA.
Wereszczynski
Jeff
J
Andricioaei
Ioan
I
D003198:Computer Simulation; D017276:Friction; D007700:Kinetics; D015233:Models, Statistical; D013816:Thermodynamics