.. index:: bond_style oxdna/fene
.. index:: bond_style oxdna2/fene
.. index:: bond_style oxrna2/fene

bond_style oxdna/fene command
=============================

bond_style oxdna2/fene command
==============================

bond_style oxrna2/fene command
==============================

Syntax
""""""

.. code-block:: LAMMPS

   bond_style oxdna/fene

   bond_style oxdna2/fene

   bond_style oxrna2/fene

Examples
""""""""

.. code-block:: LAMMPS

   # LJ units
   bond_style oxdna/fene
   bond_coeff * 2.0 0.25 0.7525

   bond_style oxdna2/fene
   bond_coeff * 2.0 0.25 0.7564

   bond_style oxrna2/fene
   bond_coeff * 2.0 0.25 0.76107

   bond_style oxdna/fene
   bond_coeff * oxdna_lj.cgdna

   # Real units
   bond_style oxdna/fene
   bond_coeff * 11.92337812042065 2.1295 6.409795

   bond_style oxdna2/fene
   bond_coeff * 11.92337812042065 2.1295 6.4430152

   bond_style oxrna2/fene
   bond_coeff * 11.92337812042065 2.1295 6.482800913

   bond_style oxrna2/fene
   bond_coeff * oxrna2_real.cgdna

.. note::

   The coefficients in the above examples have to be kept fixed and
   cannot be changed without reparameterizing the entire model. They are
   provided in forms compatible with both *units lj* and *units real*
   (see documentation of :doc:`units <units>`).  These can also be read
   from a potential file with correct unit style by specifying the name
   of the file. Several potential files for each unit style are included
   in the ``potentials`` directory of the LAMMPS distribution.

Description
"""""""""""

The *oxdna/fene*, *oxdna2/fene*, and *oxrna2/fene* bond styles use the potential

.. 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) <Ouldridge0>` to model the connectivity of
the phosphate backbone in the oxDNA/oxRNA force field for coarse-grained
modelling of DNA/RNA.

The following coefficients must be defined for the bond type via the
:doc:`bond_coeff <bond_coeff>` command as given in the above example, or
in the data file or restart files read by the :doc:`read_data
<read_data>` or :doc:`read_restart <read_restart>` commands:

* :math:`\epsilon` (energy)
* :math:`\Delta` (distance)
* :math:`r_0` (distance)

.. 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 :doc:`pair_style
   oxdna/excv <pair_oxdna>`). For the oxDNA2 :ref:`(Snodin) <Snodin0>`
   bond style the analogous pair styles *oxdna2/excv* , *oxdna2/stk* ,
   *oxdna2/xstk* , *oxdna2/coaxstk* , *oxdna2/hbond* and an additional
   Debye-Hueckel pair style *oxdna2/dh* have to be defined. The same
   applies to the oxRNA2 :ref:`(Sulc1) <Sulc01>` styles.

.. note::

   This bond style has to be used with the *atom_style hybrid bond
   ellipsoid oxdna* (see documentation of :doc:`atom_style
   <atom_style>`). The *atom_style oxdna* stores the 3'-to-5' polarity
   of the nucleotide strand, which is set through the bond topology in
   the data file. The first (second) atom in a bond definition is
   understood to point towards the 3'-end (5'-end) of the strand.

.. warning::

   If data files are produced with :doc:`write_data <write_data>`, then
   the :doc:`newton <newton>` command should be set to *newton on* or
   *newton off on*.  Otherwise the data files will not have the same
   3'-to-5' polarity as the initial data file. This limitation does not
   apply to binary restart files produced with :doc:`write_restart
   <write_restart>`.

Example input and data files for DNA and RNA duplexes can be found in
``examples/PACKAGES/cgdna/examples/oxDNA/`, `.../oxDNA2/`` and
``.../oxRNA2/``.  A simple python setup tool which creates single
straight or helical DNA strands, DNA/RNA duplexes or arrays of DNA/RNA
duplexes can be found in ``examples/PACKAGES/cgdna/util/``.

Please cite :ref:`(Henrich) <Henrich0>` in any publication that uses
this implementation. An updated documentation that contains general information
on the model, its implementation and performance as well as the structure of
the data and input file can be found `here <PDF/CG-DNA.pdf>`_.

Please cite also the relevant oxDNA/oxRNA publications. These are
:ref:`(Ouldridge) <Ouldridge0>` and
:ref:`(Ouldridge-DPhil) <Ouldridge-DPhil0>` for oxDNA,
:ref:`(Snodin) <Snodin0>` for oxDNA2,
:ref:`(Sulc1) <Sulc01>` for oxRNA2
and for sequence-specific hydrogen-bonding and stacking interactions
:ref:`(Sulc2) <Sulc02>`.

----------

Potential file reading
""""""""""""""""""""""

For each style oxdna, oxdna2 and oxrna2, the first parameter argument
can be a filename, and if it is, no further arguments should be
supplied. Therefore the following command:

.. code-block:: LAMMPS

   bond_style oxdna/fene
   bond_coeff * oxdna_lj.cgdna

will be interpreted as a request to read the (FENE) potential
:ref:`(Ouldridge) <Ouldridge0>` parameters from the file with the given
name.  The file can define multiple potential parameters for both bonded
and pair interactions, but for the above bonded interactions there must
exist in the file a line of the form:

.. code-block:: LAMMPS

   *   fene    epsilon delta r0

There are sample potential files for each unit style in the
``potentials`` directory of the LAMMPS distribution. The potential file
unit system must align with the units defined via the :doc:`units
<units>` command. For conversion between different *LJ* and *real* unit
systems for oxDNA, the python tool *lj2real.py* located in the
``examples/PACKAGES/cgdna/util/`` directory can be used. This tool
assumes similar file structure to the examples found in
``examples/PACKAGES/cgdna/examples/``.

----------

Restrictions
""""""""""""

This bond style can only be used if LAMMPS was built with the
CG-DNA package and the MOLECULE and ASPHERE package.  See the
:doc:`Build package <Build_package>` page for more info.

Related commands
""""""""""""""""

:doc:`pair_style oxdna/excv <pair_oxdna>`, :doc:`pair_style oxdna2/excv <pair_oxdna2>`, :doc:`pair_style oxrna2/excv <pair_oxrna2>`,
:doc:`bond_coeff <bond_coeff>`, :doc:`atom_style oxdna <atom_style>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`

Default
"""""""


none

----------

.. _Henrich0:

**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).

.. _Ouldridge-DPhil0:

**(Ouldridge-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).

.. _Ouldridge0:

**(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).

.. _Snodin0:

**(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).

.. _Sulc01:

**(Sulc1)** P. Sulc, F. Romano, T. E. Ouldridge, et al., J. Chem. Phys. 140, 235102 (2014).

.. _Sulc02:

**(Sulc2)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
