Accelerating the Ensemble Convergence of RNA Hairpin Simulations with a Replica Exchange Structure Reservoir.

ABSTRACT: RNA is a key participant in many biological processes, but studies of RNA using computer simulations lag behind those of proteins, largely due to less-developed force fields and the slow dynamics of RNA. Generating converged RNA ensembles for force field development and other studies remains a challenge. In this study, we explore the ability of replica exchange molecular dynamics to obtain well-converged conformational ensembles for two RNA hairpin systems in an implicit solvent. Even for these small model systems, standard REMD remains computationally costly, but coupling to a pre-generated structure library using the reservoir REMD approach provides a dramatic acceleration of ensemble convergence for both model systems. Such precise ensembles could facilitate RNA force field development

SUBMITTER: Lam K 

PROVIDER: S-EPMC10658646 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature