Loading doc/src/PDF/USER-CGDNA-overview.pdf +252 B (3.27 MiB) File changed.No diff preview for this file type. View original file View changed file doc/src/Section_packages.txt +12 −8 Original line number Diff line number Diff line Loading @@ -1140,7 +1140,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library "USER-ATC"_#USER-ATC, atom-to-continuum coupling, Jones & Templeton & Zimmerman (1), "fix atc"_fix_atc.html, USER/atc, "atc"_atc, lib/atc "USER-AWPMD"_#USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, -, lib/awpmd "USER-CG-CMM"_#USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cg-cmm, "cg"_cg, - "USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, Oliver Henrich (U Edinburgh), src/USER-CGDNA/README, USER/cgdna, -, - "USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, Oliver Henrich (U Strathclyde Glasgow), src/USER-CGDNA/README, USER/cgdna, -, - "USER-COLVARS"_#USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (2), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars "USER-DIFFRACTION"_#USER-DIFFRACTION, virutal x-ray and electron diffraction, Shawn Coleman (ARL),"compute xrd"_compute_xrd.html, USER/diffraction, -, - "USER-DPD"_#USER-DPD, reactive dissipative particle dynamics (DPD), Larentzos & Mattox & Brennan (5), src/USER-DPD/README, USER/dpd, -, - Loading Loading @@ -1288,25 +1288,29 @@ him directly if you have questions. USER-CGDNA package :link(USER-CGDNA),h5 Contents: The CGDNA package implements coarse-grained force fields for single- and double-stranded DNA. This is at the moment mainly the oxDNA model, developed by Doye, Louis and Ouldridge at the University single- and double-stranded DNA. These are at the moment mainly the oxDNA and oxDNA2 models, developed by Doye, Louis and Ouldridge at the University of Oxford. The package also contains Langevin-type rigid-body integrators with improved stability. See these doc pages to get started: "bond_style oxdna/fene"_bond_oxdna.html "bond_style oxdna2/fene"_bond_oxdna.html "pair_style oxdna/..."_pair_oxdna.html "pair_style oxdna2/..."_pair_oxdna2.html "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul Supporting info: /src/USER-CGDNA/README, "bond_style oxdna/fene"_bond_oxdna.html, "pair_style oxdna/..."_pair_oxdna.html, "fix oxdna/fene"_bond_oxdna.html, "bond_style oxdna2/fene"_bond_oxdna.html, "pair_style oxdna/..."_pair_oxdna.html, "pair_style oxdna2/..."_pair_oxdna2.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html Author: Oliver Henrich at the University of Edinburgh, UK (o.henrich at epcc.ed.ac.uk or ohenrich at ph.ed.ac.uk). Contact him directly if you have any questions. Author: Oliver Henrich at the University of Strathclyde, Glasgow, UK and University of Edinburgh (ohenrich@ph.ed.ac.uk). Contact him directly if you have any questions. :line Loading doc/src/bond_oxdna.txt +16 −5 Original line number Diff line number Diff line Loading @@ -7,19 +7,24 @@ :line bond_style oxdna/fene command :h3 bond_style oxdna2/fene command :h3 [Syntax:] bond_style oxdna/fene :pre bond_style oxdna2/fene :pre [Examples:] bond_style oxdna/fene bond_coeff * 2.0 0.25 0.7525 :pre bond_style oxdna2/fene bond_coeff * 2.0 0.25 0.7564 :pre [Description:] The {oxdna/fene} bond style uses the potential The {oxdna/fene} and {oxdna2/fene} bond styles use the potential :c,image(Eqs/bond_oxdna_fene.jpg) Loading @@ -36,13 +41,16 @@ epsilon (energy) Delta (distance) r0 (distance) :ul NOTE: This bond style has to be used together with the corresponding oxDNA pair styles NOTE: The oxDNA bond style has to be used together with the corresponding oxDNA pair styles for excluded volume interaction {oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk} and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of "pair_style oxdna/excv"_pair_oxdna.html). The coefficients "pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2 "(Snodin)"_#oxdna2 bond style the analogous pair styles and an additional Debye-Hueckel pair style {oxdna2/dh} have to be defined. The coefficients in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model. Example input and data files can be found in examples/USER/cgdna/examples/duplex1/ and /duplex2/. 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, Loading @@ -60,7 +68,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. [Related commands:] "pair_style oxdna/excv"_pair_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html "pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html [Default:] none Loading @@ -68,3 +76,6 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. :link(oxdna_fene) [(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011). :link(oxdna2) [(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015). doc/src/bonds.txt +1 −0 Original line number Diff line number Diff line Loading @@ -16,6 +16,7 @@ Bond Styles :h1 bond_none bond_nonlinear bond_oxdna bond_oxdna2 bond_quartic bond_table bond_zero Loading doc/src/pair_oxdna.txt +24 −12 Original line number Diff line number Diff line Loading @@ -14,15 +14,23 @@ pair_style oxdna/coaxstk command :h3 [Syntax:] pair_style style :pre pair_style style1 :pre style = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk} :ul pair_coeff * * style2 args :pre style1 = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk} :ul style2 = {oxdna/stk} args = list of arguments for these two particular styles :ul {oxdna2/stk} args = T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 T = temperature (oxDNA units, 0.1 = 300 K) :pre [Examples:] pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 pair_coeff * * oxdna/stk 1.61048 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 pair_coeff * * oxdna/stk 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 pair_coeff * * oxdna/hbond 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 1 4 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 2 3 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 Loading @@ -42,15 +50,19 @@ The exact functional form of the pair styles is rather complex, which manifests in the above example. The individual potentials consist of products of modulation factors, which themselves are constructed from a number of more basic potentials (Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms. We refer to "(Ouldridge-DPhil)"_#Ouldridge-DPhil and "(Ouldridge)"_#Ouldridge We refer to "(Ouldridge-DPhil)"_#Ouldridge-DPhil1 and "(Ouldridge)"_#Ouldridge1 for a detailed description of the oxDNA force field. NOTE: These pair styles have to be used together with the related oxDNA bond style {oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of "bond_style oxdna/fene"_bond_oxdna.html). The coefficients "bond_style oxdna/fene"_bond_oxdna.html). With one exception the coefficients in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model. The exception is the first coefficient after {oxdna/stk} (T=0.1 in the above example). When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html the temperature coefficients have to be matched to the one used in the fix. Example input and data files can be found in examples/USER/cgdna/examples/duplex1/ and /duplex2/. 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, Loading @@ -67,14 +79,14 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. [Related commands:] "bond_style oxdna/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html "bond_style oxdna/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html, "bond_style oxdna2/fene"_bond_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html [Default:] none :line :link(Ouldridge-DPhil) :link(Ouldridge-DPhil1) [(Ouldrigde-DPhil)] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011). :link(Ouldridge) :link(Ouldridge1) [(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011). Loading
doc/src/PDF/USER-CGDNA-overview.pdf +252 B (3.27 MiB) File changed.No diff preview for this file type. View original file View changed file
doc/src/Section_packages.txt +12 −8 Original line number Diff line number Diff line Loading @@ -1140,7 +1140,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library "USER-ATC"_#USER-ATC, atom-to-continuum coupling, Jones & Templeton & Zimmerman (1), "fix atc"_fix_atc.html, USER/atc, "atc"_atc, lib/atc "USER-AWPMD"_#USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, -, lib/awpmd "USER-CG-CMM"_#USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cg-cmm, "cg"_cg, - "USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, Oliver Henrich (U Edinburgh), src/USER-CGDNA/README, USER/cgdna, -, - "USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, Oliver Henrich (U Strathclyde Glasgow), src/USER-CGDNA/README, USER/cgdna, -, - "USER-COLVARS"_#USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (2), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars "USER-DIFFRACTION"_#USER-DIFFRACTION, virutal x-ray and electron diffraction, Shawn Coleman (ARL),"compute xrd"_compute_xrd.html, USER/diffraction, -, - "USER-DPD"_#USER-DPD, reactive dissipative particle dynamics (DPD), Larentzos & Mattox & Brennan (5), src/USER-DPD/README, USER/dpd, -, - Loading Loading @@ -1288,25 +1288,29 @@ him directly if you have questions. USER-CGDNA package :link(USER-CGDNA),h5 Contents: The CGDNA package implements coarse-grained force fields for single- and double-stranded DNA. This is at the moment mainly the oxDNA model, developed by Doye, Louis and Ouldridge at the University single- and double-stranded DNA. These are at the moment mainly the oxDNA and oxDNA2 models, developed by Doye, Louis and Ouldridge at the University of Oxford. The package also contains Langevin-type rigid-body integrators with improved stability. See these doc pages to get started: "bond_style oxdna/fene"_bond_oxdna.html "bond_style oxdna2/fene"_bond_oxdna.html "pair_style oxdna/..."_pair_oxdna.html "pair_style oxdna2/..."_pair_oxdna2.html "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul Supporting info: /src/USER-CGDNA/README, "bond_style oxdna/fene"_bond_oxdna.html, "pair_style oxdna/..."_pair_oxdna.html, "fix oxdna/fene"_bond_oxdna.html, "bond_style oxdna2/fene"_bond_oxdna.html, "pair_style oxdna/..."_pair_oxdna.html, "pair_style oxdna2/..."_pair_oxdna2.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html Author: Oliver Henrich at the University of Edinburgh, UK (o.henrich at epcc.ed.ac.uk or ohenrich at ph.ed.ac.uk). Contact him directly if you have any questions. Author: Oliver Henrich at the University of Strathclyde, Glasgow, UK and University of Edinburgh (ohenrich@ph.ed.ac.uk). Contact him directly if you have any questions. :line Loading
doc/src/bond_oxdna.txt +16 −5 Original line number Diff line number Diff line Loading @@ -7,19 +7,24 @@ :line bond_style oxdna/fene command :h3 bond_style oxdna2/fene command :h3 [Syntax:] bond_style oxdna/fene :pre bond_style oxdna2/fene :pre [Examples:] bond_style oxdna/fene bond_coeff * 2.0 0.25 0.7525 :pre bond_style oxdna2/fene bond_coeff * 2.0 0.25 0.7564 :pre [Description:] The {oxdna/fene} bond style uses the potential The {oxdna/fene} and {oxdna2/fene} bond styles use the potential :c,image(Eqs/bond_oxdna_fene.jpg) Loading @@ -36,13 +41,16 @@ epsilon (energy) Delta (distance) r0 (distance) :ul NOTE: This bond style has to be used together with the corresponding oxDNA pair styles NOTE: The oxDNA bond style has to be used together with the corresponding oxDNA pair styles for excluded volume interaction {oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk} and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of "pair_style oxdna/excv"_pair_oxdna.html). The coefficients "pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2 "(Snodin)"_#oxdna2 bond style the analogous pair styles and an additional Debye-Hueckel pair style {oxdna2/dh} have to be defined. The coefficients in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model. Example input and data files can be found in examples/USER/cgdna/examples/duplex1/ and /duplex2/. 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, Loading @@ -60,7 +68,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. [Related commands:] "pair_style oxdna/excv"_pair_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html "pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html [Default:] none Loading @@ -68,3 +76,6 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. :link(oxdna_fene) [(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011). :link(oxdna2) [(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
doc/src/bonds.txt +1 −0 Original line number Diff line number Diff line Loading @@ -16,6 +16,7 @@ Bond Styles :h1 bond_none bond_nonlinear bond_oxdna bond_oxdna2 bond_quartic bond_table bond_zero Loading
doc/src/pair_oxdna.txt +24 −12 Original line number Diff line number Diff line Loading @@ -14,15 +14,23 @@ pair_style oxdna/coaxstk command :h3 [Syntax:] pair_style style :pre pair_style style1 :pre style = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk} :ul pair_coeff * * style2 args :pre style1 = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk} :ul style2 = {oxdna/stk} args = list of arguments for these two particular styles :ul {oxdna2/stk} args = T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 T = temperature (oxDNA units, 0.1 = 300 K) :pre [Examples:] pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 pair_coeff * * oxdna/stk 1.61048 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 pair_coeff * * oxdna/stk 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 pair_coeff * * oxdna/hbond 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 1 4 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 2 3 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 Loading @@ -42,15 +50,19 @@ The exact functional form of the pair styles is rather complex, which manifests in the above example. The individual potentials consist of products of modulation factors, which themselves are constructed from a number of more basic potentials (Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms. We refer to "(Ouldridge-DPhil)"_#Ouldridge-DPhil and "(Ouldridge)"_#Ouldridge We refer to "(Ouldridge-DPhil)"_#Ouldridge-DPhil1 and "(Ouldridge)"_#Ouldridge1 for a detailed description of the oxDNA force field. NOTE: These pair styles have to be used together with the related oxDNA bond style {oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of "bond_style oxdna/fene"_bond_oxdna.html). The coefficients "bond_style oxdna/fene"_bond_oxdna.html). With one exception the coefficients in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model. The exception is the first coefficient after {oxdna/stk} (T=0.1 in the above example). When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html the temperature coefficients have to be matched to the one used in the fix. Example input and data files can be found in examples/USER/cgdna/examples/duplex1/ and /duplex2/. 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, Loading @@ -67,14 +79,14 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. [Related commands:] "bond_style oxdna/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html "bond_style oxdna/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html, "bond_style oxdna2/fene"_bond_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html [Default:] none :line :link(Ouldridge-DPhil) :link(Ouldridge-DPhil1) [(Ouldrigde-DPhil)] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011). :link(Ouldridge) :link(Ouldridge1) [(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
