Asymmetric Periodic Boundary Conditions for All-Atom Molecular Dynamics and Coarse-Grained Simulations of Nucleic Acids.

ABSTRACT: Periodic boundary conditions are commonly applied in molecular dynamics simulations in the microcanonical (NVE), canonical (NVT), and isothermal-isobaric (NpT) ensembles. In their simplest application, a biological system of interest is placed in the middle of a solvation box, which is chosen 'sufficiently large' to minimize any numerical artifacts associated with the periodic boundary conditions. This practical approach brings limitations to the size of biological systems that can be simulated. Here, we study simulations of effectively infinitely long nucleic acids, which are solvated in the directions perpendicular to the polymer chain, while periodic boundary conditions are also applied along the polymer chain. We study the effects of these asymmetric periodic boundary conditions (APBC)

SUBMITTER: Erban R 

PROVIDER: S-EPMC10544013 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature