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Periodic boundary conditions are commonly applied in molecular dynamicssimulations in the microcanonical (NVE), canonical (NVT) andisothermal-isobaric (NpT) ensembles. In their simplest application, abiological system of interest is placed in the middle of a solvation box, whichis chosen 'sufficiently large' to minimize any numerical artefacts associatedwith the periodic boundary conditions. This practical approach bringslimitations to the size of biological systems that can be simulated. Here, westudy simulations of effectively infinitely-long nucleic acids, which aresolvated in the directions perpendicular to the polymer chain, while periodicboundary conditions are also applied along the polymer chain. We study theeffects of these asymmetric periodic boundary conditions (APBC) on thesimulated results, including the mechanical properties of biopolymers and theproperties of the surrounding solvent. To get some further insights into theadvantages of using the APBC, a coarse-grained worm-like chain model is firststudied, illustrating how the persistence length can be extracted from localproperties of the polymer chain, which are less affected by the APBC than someglobal averages. This is followed by all-atom molecular dynamics simulations ofDNA in ionic solutions, where we use the APBC to investigate sequence-dependentproperties of DNA molecules and properties of the surrounding solvent.

Asymmetric periodic boundary conditions for molecular dynamics and coarse-grained simulations of nucleic acids