Loading src/USER-CGDNA/README +22 −8 Original line number Diff line number Diff line Loading @@ -2,9 +2,9 @@ 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] for the individual bond and pair styles. 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 [3]. 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", Loading @@ -13,16 +13,20 @@ 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] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and [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/duplex1/ and /duplex2/. A simple python setup tool which creates single straight or helical DNA strands as well as DNA duplexes and arrays of duplexes 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 model, the structure of the input and data file, the setup tool 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. Loading @@ -35,6 +39,7 @@ of the LAMMPS manual). The creator of this package is: Dr Oliver Henrich University of Strathclyde, UK University of Edinburgh, UK ohenrich@ph.ed.ac.uk o.henrich@epcc.ed.ac.uk Loading @@ -45,6 +50,8 @@ o.henrich@epcc.ed.ac.uk 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 Loading @@ -59,6 +66,13 @@ 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" Loading Loading
src/USER-CGDNA/README +22 −8 Original line number Diff line number Diff line Loading @@ -2,9 +2,9 @@ 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] for the individual bond and pair styles. 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 [3]. 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", Loading @@ -13,16 +13,20 @@ 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] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and [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/duplex1/ and /duplex2/. A simple python setup tool which creates single straight or helical DNA strands as well as DNA duplexes and arrays of duplexes 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 model, the structure of the input and data file, the setup tool 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. Loading @@ -35,6 +39,7 @@ of the LAMMPS manual). The creator of this package is: Dr Oliver Henrich University of Strathclyde, UK University of Edinburgh, UK ohenrich@ph.ed.ac.uk o.henrich@epcc.ed.ac.uk Loading @@ -45,6 +50,8 @@ o.henrich@epcc.ed.ac.uk 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 Loading @@ -59,6 +66,13 @@ 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" Loading
