Sampling Performance of Multiple Independent Molecular Dynamics Simulations of an RNA Aptamer.

ABSTRACT: Using multiple independent simulations instead of one long simulation has been shown to improve the sampling performance attained with the molecular dynamics (MD) simulation method. However, it is generally not known how long each independent simulation should be, how many independent simulations should be used, or to what extent either of these factors affects the overall sampling performance achieved for a given system. The goal of the present study was to assess the sampling performance of multiple independent MD simulations, where each independent simulation begins from a different initial molecular conformation. For this purpose, we used an RNA aptamer that is 25 nucleotides long as a case study. The initial conformations of the aptamer are derived from six de novo predicted 3D

SUBMITTER: Yan S 

PROVIDER: S-EPMC7439393 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature