forked from lijiext/lammps
remove outdated txt files
This commit is contained in:
Axel Kohlmeyer
parent
e1849232b8
commit
d7d1d57170
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Commands_all.html)
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:line
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fix nve/dot command :h3
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[Syntax:]
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fix ID group-ID nve/dot :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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nve/dot = style name of this fix command :l
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:ule
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[Examples:]
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fix 1 all nve/dot :pre
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[Description:]
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Apply a rigid-body integrator as described in "(Davidchack)"_#Davidchack1
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to a group of atoms, but without Langevin dynamics.
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This command performs Molecular dynamics (MD)
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via a velocity-Verlet algorithm and an evolution operator that rotates
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the quaternion degrees of freedom, similar to the scheme outlined in "(Miller)"_#Miller1.
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This command is the equivalent of the "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
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without damping and noise and can be used to determine the stability range
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in a NVE ensemble prior to using the Langevin-type DOTC-integrator
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(see also "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html).
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The command is equivalent to the "fix nve"_fix_nve.html.
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The particles are always considered to have a finite size.
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An example input file can be found in /examples/USER/cgdna/examples/duplex1/.
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Further details of the implementation and stability of the integrator are contained in "(Henrich)"_#Henrich3.
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The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
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:line
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[Restrictions:]
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These pair styles can only be used if LAMMPS was built with the
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"USER-CGDNA"_Package_details.html#PKG-USER-CGDNA package and the MOLECULE and ASPHERE package.
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See the "Build package"_Build_package.html doc page for more info.
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[Related commands:]
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"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "fix nve"_fix_nve.html
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[Default:] none
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:line
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:link(Davidchack1)
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[(Davidchack)] R.L Davidchack, T.E. Ouldridge, and M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
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:link(Miller1)
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[(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
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:link(Henrich3)
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[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
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@ -1,143 +0,0 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Commands_all.html)
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:line
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fix nve/dotc/langevin command :h3
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[Syntax:]
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fix ID group-ID nve/dotc/langevin Tstart Tstop damp seed keyword value :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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nve/dotc/langevin = style name of this fix command :l
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Tstart,Tstop = desired temperature at start/end of run (temperature units) :l
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damp = damping parameter (time units) :l
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seed = random number seed to use for white noise (positive integer) :l
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keyword = {angmom} :l
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{angmom} value = factor
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factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric scale factor as discussed below :pre
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:ule
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[Examples:]
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fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10
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fix 1 all nve/dotc/langevin 0.1 0.1 78.9375 457145 angmom 10 :pre
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[Description:]
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Apply a rigid-body Langevin-type integrator of the kind "Langevin C"
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as described in "(Davidchack)"_#Davidchack2
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to a group of atoms, which models an interaction with an implicit background
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solvent. This command performs Brownian dynamics (BD)
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via a technique that splits the integration into a deterministic Hamiltonian
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part and the Ornstein-Uhlenbeck process for noise and damping.
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The quaternion degrees of freedom are updated though an evolution
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operator which performs a rotation in quaternion space, preserves
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the quaternion norm and is akin to "(Miller)"_#Miller2.
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In terms of syntax this command has been closely modelled on the
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"fix langevin"_fix_langevin.html and its {angmom} option. But it combines
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the "fix nve"_fix_nve.html and the "fix langevin"_fix_langevin.html in
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one single command. The main feature is improved stability
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over the standard integrator, permitting slightly larger timestep sizes.
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NOTE: Unlike the "fix langevin"_fix_langevin.html this command performs
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also time integration of the translational and quaternion degrees of freedom.
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The total force on each atom will have the form:
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F = Fc + Ff + Fr
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Ff = - (m / damp) v
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Fr is proportional to sqrt(Kb T m / (dt damp)) :pre
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Fc is the conservative force computed via the usual inter-particle
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interactions ("pair_style"_pair_style.html,
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"bond_style"_bond_style.html, etc).
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The Ff and Fr terms are implicitly taken into account by this fix
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on a per-particle basis.
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Ff is a frictional drag or viscous damping term proportional to the
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particle's velocity. The proportionality constant for each atom is
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computed as m/damp, where m is the mass of the particle and damp is
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the damping factor specified by the user.
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Fr is a force due to solvent atoms at a temperature T randomly bumping
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into the particle. As derived from the fluctuation/dissipation
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theorem, its magnitude as shown above is proportional to sqrt(Kb T m /
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dt damp), where Kb is the Boltzmann constant, T is the desired
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temperature, m is the mass of the particle, dt is the timestep size,
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and damp is the damping factor. Random numbers are used to randomize
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the direction and magnitude of this force as described in
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"(Dunweg)"_#Dunweg3, where a uniform random number is used (instead of
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a Gaussian random number) for speed.
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:line
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{Tstart} and {Tstop} have to be constant values, i.e. they cannot
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be variables. If used together with the oxDNA force field for
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coarse-grained simulation of DNA please note that T = 0.1 in oxDNA units
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corresponds to T = 300 K.
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The {damp} parameter is specified in time units and determines how
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rapidly the temperature is relaxed. For example, a value of 0.03
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means to relax the temperature in a timespan of (roughly) 0.03 time
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units tau (see the "units"_units.html command).
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The damp factor can be thought of as inversely related to the
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viscosity of the solvent, i.e. a small relaxation time implies a
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hi-viscosity solvent and vice versa. See the discussion about gamma
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and viscosity in the documentation for the "fix
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viscous"_fix_viscous.html command for more details.
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Note that the value 78.9375 in the second example above corresponds
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to a diffusion constant, which is about an order of magnitude larger
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than realistic ones. This has been used to sample configurations faster
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in Brownian dynamics simulations.
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The random # {seed} must be a positive integer. A Marsaglia random
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number generator is used. Each processor uses the input seed to
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generate its own unique seed and its own stream of random numbers.
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Thus the dynamics of the system will not be identical on two runs on
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different numbers of processors.
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The keyword/value option has to be used in the following way:
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This fix has to be used together with the {angmom} keyword. The
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particles are always considered to have a finite size.
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The keyword {angmom} enables thermostatting of the rotational degrees of
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freedom in addition to the usual translational degrees of freedom.
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The scale factor after the {angmom} keyword gives the ratio of the rotational to
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the translational friction coefficient.
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An example input file can be found in /examples/USER/cgdna/examples/duplex2/.
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Further details of the implementation and stability of the integrators are contained in "(Henrich)"_#Henrich4.
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The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
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:line
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[Restrictions:]
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These pair styles can only be used if LAMMPS was built with the
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"USER-CGDNA"_Package_details.html#PKG-USER-CGDNA package and the MOLECULE and ASPHERE package.
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See the "Build package"_Build_package.html doc page for more info.
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[Related commands:]
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"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html, "bond_style oxdna/fene"_bond_oxdna.html, "bond_style oxdna2/fene"_bond_oxdna.html, "pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html
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[Default:] none
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:line
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:link(Davidchack2)
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[(Davidchack)] R.L Davidchack, T.E. Ouldridge, M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
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:link(Miller2)
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[(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
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:link(Dunweg3)
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[(Dunweg)] B. Dunweg, W. Paul, Int. J. Mod. Phys. C, 2, 817-27 (1991).
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:link(Henrich4)
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[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
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@ -1,112 +0,0 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Commands_all.html)
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:line
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pair_style oxdna/excv command :h3
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pair_style oxdna/stk command :h3
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pair_style oxdna/hbond command :h3
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pair_style oxdna/xstk command :h3
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pair_style oxdna/coaxstk command :h3
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[Syntax:]
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pair_style style1 :pre
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pair_coeff * * style2 args :pre
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style1 = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk} :ul
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style2 = {oxdna/excv} or {oxdna/stk} or {oxdna/hbond} or {oxdna/xstk} or {oxdna/coaxstk}
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args = list of arguments for these particular styles :ul
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{oxdna/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
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seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
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T = temperature (oxDNA units, 0.1 = 300 K)
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xi = temperature-independent coefficient in stacking strength
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kappa = coefficient of linear temperature dependence in stacking strength
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{oxdna/hbond} args = seq eps 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
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seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
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eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs) :pre
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[Examples:]
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pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
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pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
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pair_coeff * * oxdna/stk seqdep 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
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pair_coeff * * oxdna/hbond seqdep 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
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pair_coeff 1 4 oxdna/hbond seqdep 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
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pair_coeff 2 3 oxdna/hbond seqdep 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
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pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
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pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 :pre
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[Description:]
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The {oxdna} pair styles compute the pairwise-additive parts of the oxDNA force field
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for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
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excluded volume interaction {oxdna/excv}, the stacking {oxdna/stk}, cross-stacking {oxdna/xstk}
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and coaxial stacking interaction {oxdna/coaxstk} as well
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as the hydrogen-bonding interaction {oxdna/hbond} between complementary pairs of nucleotides on
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opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
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are supported "(Sulc)"_#Sulc1. Quasi-unique base-pairing between nucleotides can be achieved by using
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more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc.
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This prevents the hybridization of in principle complementary bases within Ntypes/4 bases
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up and down along the backbone.
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The exact functional form of the pair styles is rather complex.
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The individual potentials consist of products of modulation factors,
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which themselves are constructed from a number of more basic potentials
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(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
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We refer to "(Ouldridge-DPhil)"_#Ouldridge-DPhil1 and "(Ouldridge)"_#Ouldridge1
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for a detailed description of the oxDNA force field.
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NOTE: These pair styles have to be used together with the related oxDNA bond style
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{oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of
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"bond_style oxdna/fene"_bond_oxdna.html). Most of the coefficients
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in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
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Exceptions are the first four coefficients after {oxdna/stk} (seq=seqdep, T=0.1, xi=1.3448 and kappa=2.6568 in the above example)
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and the first coefficient after {oxdna/hbond} (seq=seqdep in the above example).
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When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html
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or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
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the temperature coefficients have to be matched to the one used in the fix.
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Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
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A simple python setup tool which creates single straight or helical DNA strands,
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DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
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Please cite "(Henrich)"_#Henrich1 and the relevant oxDNA articles in any publication that uses this implementation.
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The article contains more information on the model, the structure of the input file, the setup tool
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and the performance of the LAMMPS-implementation of oxDNA.
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The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
|
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:line
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[Restrictions:]
|
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|
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These pair styles can only be used if LAMMPS was built with the
|
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USER-CGDNA package and the MOLECULE and ASPHERE package. See the
|
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"Build package"_Build_package.html doc page for more info.
|
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|
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[Related commands:]
|
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|
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"bond_style oxdna/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html,
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"bond_style oxdna2/fene"_bond_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html
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[Default:] none
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:line
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:link(Henrich1)
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[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
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:link(Sulc1)
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[(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
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:link(Ouldridge-DPhil1)
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[(Ouldrigde-DPhil)] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
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:link(Ouldridge1)
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[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
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@ -1,121 +0,0 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
|
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:link(ld,Manual.html)
|
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:link(lc,Commands_all.html)
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:line
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pair_style oxdna2/excv command :h3
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pair_style oxdna2/stk command :h3
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pair_style oxdna2/hbond command :h3
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pair_style oxdna2/xstk command :h3
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pair_style oxdna2/coaxstk command :h3
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pair_style oxdna2/dh command :h3
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[Syntax:]
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|
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pair_style style1 :pre
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pair_coeff * * style2 args :pre
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|
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style1 = {hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh} :ul
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style2 = {oxdna2/excv} or {oxdna2/stk} or {oxdna2/hbond} or {oxdna2/xstk} or {oxdna2/coaxstk} or {oxdna2/dh}
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args = list of arguments for these particular styles :ul
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{oxdna2/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
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seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
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T = temperature (oxDNA units, 0.1 = 300 K)
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xi = temperature-independent coefficient in stacking strength
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kappa = coefficient of linear temperature dependence in stacking strength
|
||||
{oxdna2/hbond} args = seq eps 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
|
||||
seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
|
||||
eps = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs)
|
||||
{oxdna2/dh} args = T rhos qeff
|
||||
T = temperature (oxDNA units, 0.1 = 300 K)
|
||||
rhos = salt concentration (mole per litre)
|
||||
qeff = effective charge (elementary charges) :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 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 * * oxdna2/hbond seqdep 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 oxdna2/hbond seqdep 1.0678 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 oxdna2/hbond seqdep 1.0678 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 * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh 0.1 1.0 0.815 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {oxdna2} pair styles compute the pairwise-additive parts of the oxDNA force field
|
||||
for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
|
||||
excluded volume interaction {oxdna2/excv}, the stacking {oxdna2/stk}, cross-stacking {oxdna2/xstk}
|
||||
and coaxial stacking interaction {oxdna2/coaxstk}, electrostatic Debye-Hueckel interaction {oxdna2/dh}
|
||||
as well as the hydrogen-bonding interaction {oxdna2/hbond} between complementary pairs of nucleotides on
|
||||
opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
|
||||
are supported "(Sulc)"_#Sulc2. Quasi-unique base-pairing between nucleotides can be achieved by using
|
||||
more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc.
|
||||
This prevents the hybridization of in principle complementary bases within Ntypes/4 bases
|
||||
up and down along the backbone.
|
||||
|
||||
The exact functional form of the pair styles is rather complex.
|
||||
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 "(Snodin)"_#Snodin and the original oxDNA publications "(Ouldridge-DPhil)"_#Ouldridge-DPhil2
|
||||
and "(Ouldridge)"_#Ouldridge2 for a detailed description of the oxDNA2 force field.
|
||||
|
||||
NOTE: These pair styles have to be used together with the related oxDNA2 bond style
|
||||
{oxdna2/fene} for the connectivity of the phosphate backbone (see also documentation of
|
||||
"bond_style oxdna2/fene"_bond_oxdna.html). Most of the coefficients
|
||||
in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
|
||||
Exceptions are the first four coefficients after {oxdna2/stk} (seq=seqdep, T=0.1, xi=1.3523 and kappa=2.6717 in the above example),
|
||||
the first coefficient after {oxdna2/hbond} (seq=seqdep in the above example) and the three coefficients
|
||||
after {oxdna2/dh} (T=0.1, rhos=1.0, qeff=0.815 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 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/.
|
||||
|
||||
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
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
These pair styles can only be used if LAMMPS was built with the
|
||||
USER-CGDNA package and the MOLECULE and ASPHERE package. See the
|
||||
"Build package"_Build_package.html doc page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"bond_style oxdna2/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, "pair_style oxdna/excv"_pair_oxdna.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
: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).
|
||||
|
||||
:link(Snodin)
|
||||
[(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
|
||||
|
||||
:link(Ouldridge-DPhil2)
|
||||
[(Ouldrigde-DPhil)] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
|
||||
|
||||
:link(Ouldridge2)
|
||||
[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
|
||||
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Reference in New Issue