Source code for the coarse-grained dsDNA model in LAMMPS.

For details see our Soft Matter paper:
Y. A. G. Fosado, D. Michieletto, J. Allan, C. A. Brackley, O. Henrich and D. Marenduzzo "A single nucleotide resolution model for large-scale simulations of double stranded DNA" Soft Matter 12 9458-9470 (2016) Soft Matter arXiv

Minimal requirements to get started with the linear and ring DNA molecules can be found in the source files as a tar ball:
cg_dsDNA.tar
This has been tested using 11-Aug-17 version of lammps.
Make sure that the ASPHERE, RIGID, USER-MISC and MOLECULE packages are installed. These are standard packages that come with lammps, and can be enabled e.g. with the command:
make yes-asphere
before compiling.

We model dsDNA as made of two bead-spring polymers, each representing one single-stranded DNA. In order to couple the two strands into a double-helix, patches are attached to the beads and interaction potentials are assigned to reproduce the geometry of a B-DNA molecule. All these potentials are described in detail in our paper. However, a brief explanation of the implementation in LAMMPS is provided in the README files inside cg_dsDNA.tar.