diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 85fb9f7e9eb54409052112f522f37dede9a1e721..6c68955bc9f8eeb646a88f7dfd617df4119c8146 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -464,6 +464,7 @@ pair_nb3b_harmonic.html
pair_nm.html
pair_none.html
pair_oxdna.html
+pair_oxdna2.html
pair_peri.html
pair_polymorphic.html
pair_quip.html
diff --git a/src/USER-CGDNA/Install.sh b/src/USER-CGDNA/Install.sh
index 0726158779e268a5a12b7222f971d3212abce3db..a0721d5bdea55ff354c046a85c46e0e06c05c3d4 100644
--- a/src/USER-CGDNA/Install.sh
+++ b/src/USER-CGDNA/Install.sh
@@ -29,19 +29,29 @@ action () {
# list of files with dependcies
action bond_oxdna_fene.cpp bond_fene.h
+action bond_oxdna2_fene.cpp bond_fene.h
action bond_oxdna_fene.h bond_fene.h
+action bond_oxdna2_fene.h bond_fene.h
action fix_nve_dotc_langevin.cpp atom_vec_ellipsoid.h
action fix_nve_dotc_langevin.h atom_vec_ellipsoid.h
action fix_nve_dot.cpp atom_vec_ellipsoid.h
action fix_nve_dot.h atom_vec_ellipsoid.h
action mf_oxdna.h atom_vec_ellipsoid.h
action pair_oxdna_coaxstk.cpp atom_vec_ellipsoid.h
+action pair_oxdna2_coaxstk.cpp atom_vec_ellipsoid.h
action pair_oxdna_coaxstk.h atom_vec_ellipsoid.h
+action pair_oxdna2_coaxstk.h atom_vec_ellipsoid.h
action pair_oxdna_excv.cpp atom_vec_ellipsoid.h
+action pair_oxdna2_excv.cpp atom_vec_ellipsoid.h
action pair_oxdna_excv.h atom_vec_ellipsoid.h
+action pair_oxdna2_excv.h atom_vec_ellipsoid.h
action pair_oxdna_hbond.cpp atom_vec_ellipsoid.h
action pair_oxdna_hbond.h atom_vec_ellipsoid.h
action pair_oxdna_stk.cpp atom_vec_ellipsoid.h
+action pair_oxdna2_stk.cpp atom_vec_ellipsoid.h
action pair_oxdna_stk.h atom_vec_ellipsoid.h
+action pair_oxdna2_stk.h atom_vec_ellipsoid.h
action pair_oxdna_xstk.cpp atom_vec_ellipsoid.h
action pair_oxdna_xstk.h atom_vec_ellipsoid.h
+action pair_oxdna2_dh.cpp atom_vec_ellipsoid.h
+action pair_oxdna2_dh.h atom_vec_ellipsoid.h
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"