Extending molecular dynamics time scales with milestoning:Example of complex kinetics In a solvated peptide

摘要

A recently introduced computational algorithm to extend time scales of atomically detailed simulations is illustrated.The algorithm,milestoning,is based on partitioning the dynamics to a sequence of trajectories between "milestones" and constructing a non-Markovian model for the motion along a reaction coordinate.The kinetics of a conformational transition in a blocked alanine is computed and shown to be accurate,more efficient than straightforward molecular dynamics by a factor of about 9,and nonexponential.A general scaling argument predicts a linear speedup with the number of milestones for diffusive processes and an exponential speedup for transitions over barriers.The algorithm is also trivial to parallelize.As a side result,milestoning also produces the free energy profile along the reaction coordinate and is able to describe nonequilibrium motions along one(or a few)degrees of freedom.