A skewed-momenta method to efficiently generate conformational-transition trajectories.
We present a novel computational method, the skewed-momenta method (Skew'M), which applies a bias to the Maxwell distribution of initial momenta used to generate ensembles of trajectories. As a result, conformational transitions are accentuated and kinetic properties are calculated more effectively. The connection to the related puddle jumping method is discussed. A reweighting scheme permits the exact calculation of kinetic properties. Applications are presented for the rapid calculation of rate constants for molecular isomerization, and for the efficient reconstruction of free-energy profiles using a straightforward modification of the Jarzynski identity.
MacFadyen
James
J
Department of Chemistry and The Program in Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA.
Andricioaei
Ioan
I
D002627:Chemistry, Physical / Q000379:methods*; D003198:Computer Simulation; D019277:Entropy; D007700:Kinetics; D008956:Models, Chemical; D015233:Models, Statistical; D008962:Models, Theoretical; D008968:Molecular Conformation; D013696:Temperature; D013816:Thermodynamics; D013997:Time Factors