A skewed-momenta method to efficiently generate conformational-transition trajectories

摘要

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.