Loading src/USER-CGDNA/README +44 −30 Original line number Diff line number Diff line Loading @@ -2,12 +2,12 @@ This package contains a LAMMPS implementation of coarse-grained models of DNA, which can be used to model sequence-specific DNA strands. Please cite [1] and the relevant oxDNA articles in any publication that uses this package. Please cite [1] and the relevant oxDNA, oxDNA2 and oxRNA2 articles in any publication that uses this package. See the doc pages and [2,3,4] for the individual bond and pair styles. 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 [5]. 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", Loading @@ -17,24 +17,31 @@ Eur. Phys. J. E 41, 57 (2018). 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). [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). [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] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and [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/ 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 /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 Loading @@ -54,9 +61,12 @@ 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 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_oxdna2_fene.cpp: corresponding bond style in oxDNA2 (see [3]) bond_oxrna2_fene.cpp: corresponding bond style in oxRNA2 (see [5]) ** Pair styles provided by this package: Loading @@ -72,16 +82,20 @@ 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 [3]) 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 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] in above Ref. [7] fix_nve_dot.cpp: NVE-type rigid body integrator without noise Loading
src/USER-CGDNA/README +44 −30 Original line number Diff line number Diff line Loading @@ -2,12 +2,12 @@ This package contains a LAMMPS implementation of coarse-grained models of DNA, which can be used to model sequence-specific DNA strands. Please cite [1] and the relevant oxDNA articles in any publication that uses this package. Please cite [1] and the relevant oxDNA, oxDNA2 and oxRNA2 articles in any publication that uses this package. See the doc pages and [2,3,4] for the individual bond and pair styles. 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 [5]. 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", Loading @@ -17,24 +17,31 @@ Eur. Phys. J. E 41, 57 (2018). 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). [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). [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] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and [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/ 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 /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 Loading @@ -54,9 +61,12 @@ 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 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_oxdna2_fene.cpp: corresponding bond style in oxDNA2 (see [3]) bond_oxrna2_fene.cpp: corresponding bond style in oxRNA2 (see [5]) ** Pair styles provided by this package: Loading @@ -72,16 +82,20 @@ 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 [3]) 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 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] in above Ref. [7] fix_nve_dot.cpp: NVE-type rigid body integrator without noise
