diff --git a/src/USER-CGDNA/README b/src/USER-CGDNA/README index 8158b83ab80c0943c9ca58ab918fbb8122ca153b..516f18c36cc67c1dec308bf8cd5114a0a1e7e3d9 100644 --- a/src/USER-CGDNA/README +++ b/src/USER-CGDNA/README @@ -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", @@ -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/util/. A technical report with more information -on the model, the structure of the input and data file, the setup tool +/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. @@ -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 @@ -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 @@ -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"