A local resampling trick for focused molecular dynamics
Statistical Mechanics
2023-08-28 v2 Computational Physics
Computation
Abstract
We describe a method that focuses sampling effort on a user-defined selection of a large system, which can lead to substantial decreases in computational effort by speeding up the calculation of nonbonded interactions. A naive approach can lead to incorrect sampling if the selection depends on the configuration in a way that is not accounted for. We avoid this pitfall by introducing appropriate auxiliary variables. This results in an implementation that is closely related to configurational freezing and elastic barrier dynamical freezing. We implement the method and validate that it can be used to supplement conventional molecular dynamics in free energy calculations (absolute hydration and relative binding).
Cite
@article{arxiv.2305.05475,
title = {A local resampling trick for focused molecular dynamics},
author = {Joshua Fass and Forrest York and Matthew Wittmann and Joseph Kaus and Yutong Zhao},
journal= {arXiv preprint arXiv:2305.05475},
year = {2023}
}