A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and Pitfalls.

ABSTRACT: The string method with swarms of trajectories (SMwST) is an algorithm that identifies a physically meaningful transition pathway─a one-dimensional curve, embedded within a high-dimensional space of selected collective variables. The SMwST algorithm leans on a series of short, unbiased molecular dynamics simulations spawned at different locations of the discretized path, from whence an average dynamic drift is determined to evolve the string toward an optimal pathway. However conceptually simple in both its theoretical formulation and practical implementation, the SMwST algorithm is computationally intensive and requires a careful choice of parameters for optimal cost-effectiveness in applications to challenging problems in chemistry and biology. In this contribution, the SMwST algorithm is

SUBMITTER: Chen H 

PROVIDER: S-EPMC8904302 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature