This package contains a LAMMPS implementation of coarse-grained models of DNA, which can be used to model sequence-specific DNA strands.

See the doc pages and [1,2] for the individual bond and pair styles. The packages contains also a new Langevin-type rigid-body integrator, which has also its own doc page and is explained in [3].

[1] T. Ouldridge, A. Louis, J. Doye, "Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model", J. Chem. Phys. 134, 085101 (2011).

[2] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).

[3] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and gradient thermostats for rigid body dynamics", J. Chem. Phys. 142, 144114 (2015).

Example input and data files can be found in /examples/USER/cgdna/examples/duplex1/ and /duplex2/. A simple python setup tool which creates single straight or helical DNA strands as well as DNA duplexes and arrays of duplexes can be found in /examples/USER/cgdna/util/. A technical report with more information on the model, the structure of the input and data file, the setup tool and the performance of the LAMMPS-implementation of oxDNA can be found in /doc/src/PDF/USER-CGDNA-overview.pdf.

IMPORTANT NOTE: This package can only be used if LAMMPS is compiled with the MOLECULE and ASPHERE packages. These should be included in the LAMMPS build by typing "make yes-asphere yes-molecule" prior to the usual compilation (see the "Including/excluding packages" section of the LAMMPS manual).

The creator of this package is:

Dr Oliver Henrich University of Edinburgh, UK ohenrich@ph.ed.ac.uk o.henrich@epcc.ed.ac.uk

• Bond styles provided by this package:

bond_oxdna_fene.cpp: backbone connectivity, a modified FENE potential

• Pair styles provided by this package:

pair_oxdna_excv.cpp: excluded volume interaction between the nucleotides

pair_oxdna_stk.cpp: stacking interaction between consecutive nucleotides

on the same strand

pair_oxdna_hbond.cpp: hydrogen-bonding interaction between complementary

nucleotides on different strands, e.g. A-T and C-G

pair_oxdna_xstk.cpp: cross-stacking interaction between nucleotides

pair_oxdna_coaxstk.cpp: coaxial stacking interaction between nucleotides

• Fixes provided by this package:

fix_nve_dotc_langevin.cpp: fix for Langevin-type rigid body integrator "C"

in above Ref. [3]

fix_nve_dot.cpp: NVE-type rigid body integrator without noise