160 lines
5.1 KiB
ReStructuredText
160 lines
5.1 KiB
ReStructuredText
.. 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
|
|
|
|
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
|
|
|
|
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.
|
|
The coefficients in the above example have to be kept fixed and cannot
|
|
be changed without reparameterizing the entire model.
|
|
|
|
.. 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>`.
|
|
|
|
----------
|
|
|
|
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).
|