Benchmarking the Drude Polarizable Force Field Using the r(GACC) Tetranucleotide.

ABSTRACT: Polarizable force fields, in particular, the Drude polarizable force field (Drude FF), may hold the key to more accurately modeling biomolecules with molecular dynamics simulations by explicitly accounting for atomic polarizability. Previous work has shown promising results in simulating duplex nucleic acids and protein structures with excellent agreement with experimental values. However, benchmarking the Drude polarizable force field with highly flexible, single-stranded structures has yet to be achieved. In this work, the r(GACC) tetranucleotide is simulated over a multimicrosecond time scale, starting with various different initial conformations. Despite the starting conformation, including starting from the expected dominant A-form major conformation, the experimental structural distr

SUBMITTER: Winkler L 

PROVIDER: S-EPMC10131218 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature