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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.

Please cite

DOI

as well as [1] 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 [7].

[1] 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).

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

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

[4] 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).

[5] P. Sulc, F. Romano, T.E. Ouldridge, et al., "A nucleotide-level coarse-grained model of RNA", J. Chem. Phys. 140, 235102 (2014).

[6] P. Sulc, F. Romano, T.E. Ouldridge, et al., "Sequence-dependent thermodynamics of a coarse-grained DNA model", J. Chem. Phys. 137, 135101 (2012).

[7] 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 [4])

bond_oxrna2_fene.cpp: corresponding bond style in oxRNA2 (see [5])

** 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 [4])

pair_oxrna2_excv.cpp, pair_oxrna2_stk.cpp, pair_oxrna2_hbond.cpp, pair_oxrna2_xstk.cpp: corresponding pair styles in oxDNA2 (see [5])

pair_oxdna2_dh.cpp, pair_oxrna2_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. [7]

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

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