Extending molecular dynamics time scales with milestoning: example of complex kinetics in a solvated peptide.
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.
West
Anthony M A
AM
Department of Physics, Cornell University, Ithaca, New York 14853, USA.
Elber
Ron
R
Shalloway
David
D
D000465:Algorithms; D003198:Computer Simulation; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D044367:Phase Transition; D011487:Protein Conformation; D012997:Solvents / Q000737:chemistry*
D010455:Peptides; D012997:Solvents