This package contains a LAMMPS implementation of coarse-grained models of DNA, which can be used to model sequence-specific DNA strands.
as well as  and the relevant oxDNA, oxDNA2 and oxRNA2 articles in any publication that uses this package.
See the doc pages and [2,3,4,5,6] 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 .
 O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, "Coarse-grained simulation of DNA using LAMMPS", Eur. Phys. J. E 41, 57 (2018).
 T. Ouldridge, A. Louis, J. Doye, "Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model", J. Chem. Phys. 134, 085101 (2011).
 T.E. Ouldridge, "Coarse-grained modelling of DNA and DNA self-assembly", DPhil. University of Oxford (2011).
 B.E. Snodin, F. Randisi, M. Mosayebi, et al., "Introducing Improved structural properties and salt dependence into a coarse-grained model of DNA", J. Chem. Phys. 142, 234901 (2015).
 P. Sulc, F. Romano, T.E. Ouldridge, et al., "A nucleotide-level coarse-grained model of RNA", J. Chem. Phys. 140, 235102 (2014).
 P. Sulc, F. Romano, T.E. Ouldridge, et al., "Sequence-dependent thermodynamics of a coarse-grained DNA model", J. Chem. Phys. 137, 135101 (2012).
 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/oxDNA/, /oxDNA2/ and /oxRNA2/. Python setup tools which create single straight or helical DNA or RNA strands as well as DNA or RNA duplexes or arrays of duplexes can be found in /examples/USER/cgdna/util/. A technical report with more general information on the model, its implementation and performance as well as the structure of the data and input file can be found in /doc/src/PDF/USER-CGDNA.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 Strathclyde, Glasgow, UK oliver d o t henrich a t strath d o t ac d o t uk
** Bond styles provided by this package:
bond_oxdna_fene.cpp: backbone connectivity, a modified FENE potential (see [2,3])
bond_oxdna2_fene.cpp: corresponding bond style in oxDNA2 (see )
bond_oxrna2_fene.cpp: corresponding bond style in oxRNA2 (see )
** 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
pair_oxdna2_excv.cpp, pair_oxdna2_coaxstk.cpp: corresponding pair styles in oxDNA2 (see )
pair_oxrna2_excv.cpp, pair_oxrna2_stk.cpp, pair_oxrna2_hbond.cpp, pair_oxrna2_xstk.cpp: corresponding pair styles in oxDNA2 (see )
Debye-Hueckel electrostatic interaction between backbone sites
** Fixes provided by this package:
fix_nve_dotc_langevin.cpp: fix for Langevin-type rigid body integrator "C" in above Ref. 
fix_nve_dot.cpp: NVE-type rigid body integrator without noise