diff --git a/doc/src/PDF/USER-CGDNA.pdf b/doc/src/PDF/USER-CGDNA.pdf new file mode 100644 index 0000000000..843bba00d5 Binary files /dev/null and b/doc/src/PDF/USER-CGDNA.pdf differ diff --git a/doc/src/bond_oxdna.txt b/doc/src/bond_oxdna.txt index 2add6f4c2f..7c406229a2 100644 --- a/doc/src/bond_oxdna.txt +++ b/doc/src/bond_oxdna.txt @@ -51,9 +51,11 @@ The coefficients in the above example have to be kept fixed and cannot be change Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. A simple python setup tool which creates single straight or helical DNA strands, DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/. -A technical report with more information on the model, the structure of the input file, -the setup tool and the performance of the LAMMPS-implementation of oxDNA -can be found "here"_PDF/USER-CGDNA-overview.pdf. + +Please cite "(Henrich)"_#Henrich and the relevant oxDNA articles in any publication that uses this implementation. +The article contains more information on the model, the structure of the input file, the setup tool +and the performance of the LAMMPS-implementation of oxDNA. +The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf. :line @@ -72,6 +74,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. :line +:link(Henrich) +[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018). + :link(oxdna_fene) [(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011). diff --git a/doc/src/pair_oxdna.txt b/doc/src/pair_oxdna.txt index 26a205bcf9..ad113d15b8 100644 --- a/doc/src/pair_oxdna.txt +++ b/doc/src/pair_oxdna.txt @@ -71,9 +71,11 @@ the temperature coefficients have to be matched to the one used in the fix. Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. A simple python setup tool which creates single straight or helical DNA strands, DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/. -A technical report with more information on the model, the structure of the input file, -the setup tool and the performance of the LAMMPS-implementation of oxDNA -can be found "here"_PDF/USER-CGDNA-overview.pdf. + +Please cite "(Henrich)"_#Henrich and the relevant oxDNA articles in any publication that uses this implementation. +The article contains more information on the model, the structure of the input file, the setup tool +and the performance of the LAMMPS-implementation of oxDNA. +The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf. :line @@ -92,6 +94,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. :line +:link(Henrich) +[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018). + :link(Sulc1) [(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012). diff --git a/doc/src/pair_oxdna2.txt b/doc/src/pair_oxdna2.txt index 2408c02d10..1b55031b2c 100644 --- a/doc/src/pair_oxdna2.txt +++ b/doc/src/pair_oxdna2.txt @@ -77,9 +77,11 @@ the temperature coefficients have to be matched to the one used in the fix. Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. A simple python setup tool which creates single straight or helical DNA strands, DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/. -A technical report with more information on the model, the structure of the input file, -the setup tool and the performance of the LAMMPS-implementation of oxDNA -can be found "here"_PDF/USER-CGDNA-overview.pdf. + +Please cite "(Henrich)"_#Henrich and the relevant oxDNA articles in any publication that uses this implementation. +The article contains more information on the model, the structure of the input file, the setup tool +and the performance of the LAMMPS-implementation of oxDNA. +The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf. :line @@ -98,6 +100,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. :line +:link(Henrich) +[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018). + :link(Sulc2) [(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012). diff --git a/src/USER-CGDNA/README b/src/USER-CGDNA/README index 735f005f54..d71f3b7a43 100644 --- a/src/USER-CGDNA/README +++ b/src/USER-CGDNA/README @@ -2,22 +2,29 @@ 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 [1,2,3] 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 [4]. +Please cite [1] and the relevant oxDNA articles in any publication +that uses this package. -[1] T. Ouldridge, A. Louis, J. Doye, "Structural, mechanical, +See the doc pages and [2,3,4] 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]. + +[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). -[2] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA +[3] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011). -[3] B.E. Snodin, F. Randisi, M. Mosayebi, et al., Introducing +[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] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and +[5] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and gradient thermostats for rigid body dynamics", J. Chem. Phys. 142, 144114 (2015). @@ -28,7 +35,7 @@ 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. +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 @@ -40,9 +47,8 @@ The creator of this package is: Dr Oliver Henrich University of Strathclyde, Glasgow, UK -oliver.henrich at strath.ac.uk -University of Edinburgh, UK -ohenrich at staffmail.ed.ac.uk +oliver d o t henrich a t strath d o t ac d o t uk + --------------------------------------------------------------------------