  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 artefacts 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) on the
simulated results, including the mechanical properties of biopolymers and the
properties of the surrounding solvent. To get some further insights into the
advantages of using the APBC, a coarse-grained worm-like chain model is first
studied, illustrating how the persistence length can be extracted from local
properties of the polymer chain, which are less affected by the APBC than some
global averages. This is followed by all-atom molecular dynamics simulations of
DNA in ionic solutions, where we use the APBC to investigate sequence-dependent
properties of DNA molecules and properties of the surrounding solvent.
