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 [1,2,3] 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 [4].

[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] 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).

[4] 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/ and /oxDNA2/. Python setup tools which create single straight or helical DNA strands as well as DNA duplexes or arrays of duplexes can be found in /examples/USER/cgdna/util/. A technical report with more information on the models, 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 Strathclyde, Glasgow, UK oliver.henrich at strath.ac.uk University of Edinburgh, UK ohenrich at staffmail.ed.ac.uk

• Bond styles provided by this package:

bond_oxdna_fene.cpp: backbone connectivity, a modified FENE potential

bond_oxdna2_fene.cpp: corresponding bond style in oxDNA2 (see [3])

• 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_stk.cpp, pair_oxdna2_coaxstk.cpp:

		     corresponding pair styles in oxDNA2 (see [3])

pair_oxdna2_dh.cpp: 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. [3]

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