Assessing the Current State of Amber Force Field Modifications for DNA─2023 Edition.

ABSTRACT: Advances in molecular dynamics (MD) software alongside enhanced computational power and hardware have allowed for MD simulations to significantly expand our knowledge of biomolecular structure, dynamics, and interactions. Furthermore, it has allowed for the extension of conformational sampling times from nanoseconds to the microsecond level and beyond. This has not only made convergence of conformational ensembles through comprehensive sampling possible but consequently exposed deficiencies and allowed the community to overcome limitations in the available force fields. The reproducibility and accuracy of the force fields are imperative in order to produce biologically relevant data. The Amber nucleic acid force fields have been used widely since the mid-1980s, and improvement of these for

SUBMITTER: Love O 

PROVIDER: S-EPMC10339676 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature