  During the last decade coarse-grained nucleotide models have emerged that
allow us to DNA and RNA on unprecedented time and length scales. Among them is
oxDNA, a coarse-grained, sequence-specific model that captures the
hybridisation transition of DNA and many structural properties of single- and
double-stranded DNA. oxDNA was previously only available as standalone
software, but has now been implemented into the popular LAMMPS molecular
dynamics code. This article describes the new implementation and analyses its
parallel performance. Practical applications are presented that focus on
single-stranded DNA, an area of research which has been so far
under-investigated. The LAMMPS implementation of oxDNA lowers the entry barrier
for using the oxDNA model significantly, facilitates future code development
and interfacing with existing LAMMPS functionality as well as other
coarse-grained and atomistic DNA models.
