Update docs: bond_oxdna

\documentclass[12pt]{article}

\pagestyle{empty}

\begin{document}

$$ 

  E = - \frac{\epsilon}{2} \ln \left[ 1 - \left(\frac{r-r0}{\Delta}\right)^2\right]

$$

\end{document}

.. index:: bond\_style oxdna/fene

.. index:: bond_style oxdna/fene

bond\_style oxdna/fene command

==============================

bond_style oxdna/fene command

=============================

bond\_style oxdna2/fene command

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bond_style oxdna2/fene command

==============================

Syntax

""""""

.. parsed-literal::

.. code-block:: LAMMPS

   bond_style oxdna/fene

""""""""

.. parsed-literal::

.. code-block:: LAMMPS

   bond_style oxdna/fene

   bond_coeff \* 2.0 0.25 0.7525

   bond_coeff * 2.0 0.25 0.7525

   bond_style oxdna2/fene

   bond_coeff \* 2.0 0.25 0.7564

   bond_coeff * 2.0 0.25 0.7564

Description

"""""""""""

The *oxdna/fene* and *oxdna2/fene* bond styles use the potential

.. image:: Eqs/bond_oxdna_fene.jpg

   :align: center

.. math::

   E = - \frac{\epsilon}{2} \ln \left[ 1 - \left(\frac{r-r_0}{\Delta}\right)^2\right]

to define a modified finite extensible nonlinear elastic (FENE)

potential :ref:`(Ouldridge) <oxdna_fene>` to model the connectivity of the

:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`

commands:

* epsilon (energy)

* Delta (distance)

* r0 (distance)

* :math:`\epsilon` (energy)

* :math:`\Delta` (distance)

* :math:`r_0` (distance)

.. note::

**(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al.,

J. Chem. Phys. 142, 234901 (2015).

.. _lws: http://lammps.sandia.gov

.. _ld: Manual.html

.. _lc: Commands_all.html

"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c

:link(lws,http://lammps.sandia.gov)

:link(ld,Manual.html)

:link(lc,Commands_all.html)

: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} and {oxdna2/fene} bond styles use the potential

:c,image(Eqs/bond_oxdna_fene.jpg)

to define a modified finite extensible nonlinear elastic (FENE)

potential "(Ouldridge)"_#oxdna_fene to model the connectivity of the

phosphate backbone in the oxDNA force field for coarse-grained

modelling of DNA.

The following coefficients must be defined for the bond type via the

"bond_coeff"_bond_coeff.html command as given in the above example, or

in the data file or restart files read by the

"read_data"_read_data.html or "read_restart"_read_restart.html

commands:

epsilon (energy)

Delta (distance)

r0 (distance) :ul

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). 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 reparameterizing the entire model.

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)"_#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

[Restrictions:]

This bond style 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:]

"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

: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).

:link(oxdna2)

[(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al.,

J. Chem. Phys. 142, 234901 (2015).