Loading doc/src/PDF/USER-CGDNA-overview.pdf→doc/src/PDF/USER-CGDNA.pdf +783 KiB (4.03 MiB) File changed and moved.No diff preview for this file type. View original file View changed file doc/src/bond_oxdna.txt +8 −3 Original line number Diff line number Diff line Loading @@ -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)"_#Henrich2 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 Loading @@ -72,6 +74,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. :line :link(Henrich2) [(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). Loading doc/src/pair_oxdna.txt +8 −3 Original line number Diff line number Diff line Loading @@ -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)"_#Henrich1 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 Loading @@ -92,6 +94,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. :line :link(Henrich1) [(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). Loading doc/src/pair_oxdna2.txt +8 −3 Original line number Diff line number Diff line Loading @@ -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 Loading @@ -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). Loading src/USER-CGDNA/README +16 −10 Original line number Diff line number Diff line Loading @@ -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. Please cite [1] and the relevant oxDNA articles in any publication that uses this package. 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 [4]. 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). [1] T. Ouldridge, A. Louis, J. Doye, "Structural, mechanical, [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). Loading @@ -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 Loading @@ -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 -------------------------------------------------------------------------- Loading Loading
doc/src/PDF/USER-CGDNA-overview.pdf→doc/src/PDF/USER-CGDNA.pdf +783 KiB (4.03 MiB) File changed and moved.No diff preview for this file type. View original file View changed file
doc/src/bond_oxdna.txt +8 −3 Original line number Diff line number Diff line Loading @@ -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)"_#Henrich2 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 Loading @@ -72,6 +74,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. :line :link(Henrich2) [(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). Loading
doc/src/pair_oxdna.txt +8 −3 Original line number Diff line number Diff line Loading @@ -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)"_#Henrich1 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 Loading @@ -92,6 +94,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. :line :link(Henrich1) [(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). Loading
doc/src/pair_oxdna2.txt +8 −3 Original line number Diff line number Diff line Loading @@ -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 Loading @@ -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). Loading
src/USER-CGDNA/README +16 −10 Original line number Diff line number Diff line Loading @@ -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. Please cite [1] and the relevant oxDNA articles in any publication that uses this package. 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 [4]. 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). [1] T. Ouldridge, A. Louis, J. Doye, "Structural, mechanical, [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). Loading @@ -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 Loading @@ -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 -------------------------------------------------------------------------- Loading
