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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
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** 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
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