Assessment of the DNA partial specific volume and hydration layer properties from CHARMM Drude polarizable and additive MD simulations.

ABSTRACT: In this study we report on the accurate computation of the biomolecular partial specific volume (PSV) from explicit-solvent molecular dynamics (MD) simulations. The case of DNA is considered, and the predictions from two state-of-the-art biomolecular force fields, the CHARMM36 additive (C36) and Drude polarizable models, are presented. Unlike most of the existing approaches to assess the biomolecular PSV, our proposed method bypasses the need for the arbitrarily defined volume partitioning scheme into the intrinsic solute and solvent contributions. At the same time, to assess the density of the hydration layer water, we combine our simulation analysis approach with some of the existing fixed-size methods to determine the solute's intrinsic volume, and also propose our own approach to compu

SUBMITTER: Savelyev A 

PROVIDER: S-EPMC8121142 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature