218 lines
7.0 KiB
ReStructuredText
218 lines
7.0 KiB
ReStructuredText
.. index:: bond_style oxdna/fene
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.. index:: bond_style oxdna2/fene
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.. index:: bond_style oxrna2/fene
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bond_style oxdna/fene command
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=============================
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bond_style oxdna2/fene command
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==============================
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bond_style oxrna2/fene command
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==============================
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Syntax
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""""""
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.. code-block:: LAMMPS
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bond_style oxdna/fene
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bond_style oxdna2/fene
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bond_style oxrna2/fene
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Examples
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""""""""
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.. code-block:: LAMMPS
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# LJ units
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bond_style oxdna/fene
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bond_coeff * 2.0 0.25 0.7525
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bond_style oxdna2/fene
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bond_coeff * 2.0 0.25 0.7564
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bond_style oxrna2/fene
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bond_coeff * 2.0 0.25 0.76107
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bond_style oxdna/fene
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bond_coeff * oxdna_lj.cgdna
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# Real units
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bond_style oxdna/fene
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bond_coeff * 11.92337812042065 2.1295 6.409795
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bond_style oxdna2/fene
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bond_coeff * 11.92337812042065 2.1295 6.4430152
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bond_style oxrna2/fene
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bond_coeff * 11.92337812042065 2.1295 6.482800913
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bond_style oxrna2/fene
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bond_coeff * oxrna2_real.cgdna
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.. note::
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The coefficients in the above examples have to be kept fixed and
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cannot be changed without reparameterizing the entire model. They are
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provided in forms compatible with both *units lj* and *units real*
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(see documentation of :doc:`units <units>`). These can also be read
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from a potential file with correct unit style by specifying the name
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of the file. Several potential files for each unit style are included
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in the ``potentials`` directory of the LAMMPS distribution.
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Description
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"""""""""""
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The *oxdna/fene*, *oxdna2/fene*, and *oxrna2/fene* bond styles use the potential
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.. math::
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E = - \frac{\epsilon}{2} \ln \left[ 1 - \left(\frac{r-r_0}{\Delta}\right)^2\right]
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to define a modified finite extensible nonlinear elastic (FENE)
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potential :ref:`(Ouldridge) <Ouldridge0>` to model the connectivity of
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the phosphate backbone in the oxDNA/oxRNA force field for coarse-grained
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modelling of DNA/RNA.
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The following coefficients must be defined for the bond type via the
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:doc:`bond_coeff <bond_coeff>` command as given in the above example, or
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in the data file or restart files read by the :doc:`read_data
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<read_data>` or :doc:`read_restart <read_restart>` commands:
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* :math:`\epsilon` (energy)
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* :math:`\Delta` (distance)
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* :math:`r_0` (distance)
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.. note::
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The oxDNA bond style has to be used together with the corresponding
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oxDNA pair styles for excluded volume interaction *oxdna/excv* ,
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stacking *oxdna/stk* , cross-stacking *oxdna/xstk* and coaxial
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stacking interaction *oxdna/coaxstk* as well as hydrogen-bonding
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interaction *oxdna/hbond* (see also documentation of :doc:`pair_style
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oxdna/excv <pair_oxdna>`). For the oxDNA2 :ref:`(Snodin) <Snodin0>`
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bond style the analogous pair styles *oxdna2/excv* , *oxdna2/stk* ,
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*oxdna2/xstk* , *oxdna2/coaxstk* , *oxdna2/hbond* and an additional
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Debye-Hueckel pair style *oxdna2/dh* have to be defined. The same
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applies to the oxRNA2 :ref:`(Sulc1) <Sulc01>` styles.
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.. note::
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This bond style has to be used with the *atom_style hybrid bond
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ellipsoid oxdna* (see documentation of :doc:`atom_style
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<atom_style>`). The *atom_style oxdna* stores the 3'-to-5' polarity
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of the nucleotide strand, which is set through the bond topology in
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the data file. The first (second) atom in a bond definition is
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understood to point towards the 3'-end (5'-end) of the strand.
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.. warning::
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If data files are produced with :doc:`write_data <write_data>`, then
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the :doc:`newton <newton>` command should be set to *newton on* or
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*newton off on*. Otherwise the data files will not have the same
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3'-to-5' polarity as the initial data file. This limitation does not
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apply to binary restart files produced with :doc:`write_restart
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<write_restart>`.
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Example input and data files for DNA and RNA duplexes can be found in
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``examples/PACKAGES/cgdna/examples/oxDNA/`, `.../oxDNA2/`` and
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``.../oxRNA2/``. A simple python setup tool which creates single
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straight or helical DNA strands, DNA/RNA duplexes or arrays of DNA/RNA
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duplexes can be found in ``examples/PACKAGES/cgdna/util/``.
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Please cite :ref:`(Henrich) <Henrich0>` in any publication that uses
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this implementation. An updated documentation that contains general information
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on the model, its implementation and performance as well as the structure of
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the data and input file can be found `here <PDF/CG-DNA.pdf>`_.
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Please cite also the relevant oxDNA/oxRNA publications. These are
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:ref:`(Ouldridge) <Ouldridge0>` and
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:ref:`(Ouldridge-DPhil) <Ouldridge-DPhil0>` for oxDNA,
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:ref:`(Snodin) <Snodin0>` for oxDNA2,
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:ref:`(Sulc1) <Sulc01>` for oxRNA2
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and for sequence-specific hydrogen-bonding and stacking interactions
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:ref:`(Sulc2) <Sulc02>`.
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----------
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Potential file reading
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""""""""""""""""""""""
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For each style oxdna, oxdna2 and oxrna2, the first parameter argument
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can be a filename, and if it is, no further arguments should be
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supplied. Therefore the following command:
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.. code-block:: LAMMPS
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bond_style oxdna/fene
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bond_coeff * oxdna_lj.cgdna
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will be interpreted as a request to read the (FENE) potential
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:ref:`(Ouldridge) <Ouldridge0>` parameters from the file with the given
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name. The file can define multiple potential parameters for both bonded
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and pair interactions, but for the above bonded interactions there must
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exist in the file a line of the form:
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.. code-block:: LAMMPS
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* fene epsilon delta r0
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There are sample potential files for each unit style in the
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``potentials`` directory of the LAMMPS distribution. The potential file
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unit system must align with the units defined via the :doc:`units
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<units>` command. For conversion between different *LJ* and *real* unit
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systems for oxDNA, the python tool *lj2real.py* located in the
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``examples/PACKAGES/cgdna/util/`` directory can be used. This tool
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assumes similar file structure to the examples found in
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``examples/PACKAGES/cgdna/examples/``.
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----------
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Restrictions
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""""""""""""
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This bond style can only be used if LAMMPS was built with the
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CG-DNA package and the MOLECULE and ASPHERE package. See the
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:doc:`Build package <Build_package>` page for more info.
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Related commands
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""""""""""""""""
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:doc:`pair_style oxdna/excv <pair_oxdna>`, :doc:`pair_style oxdna2/excv <pair_oxdna2>`, :doc:`pair_style oxrna2/excv <pair_oxrna2>`,
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:doc:`bond_coeff <bond_coeff>`, :doc:`atom_style oxdna <atom_style>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
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Default
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"""""""
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none
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----------
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.. _Henrich0:
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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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.. _Ouldridge-DPhil0:
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**(Ouldridge-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
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.. _Ouldridge0:
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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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.. _Snodin0:
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**(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
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.. _Sulc01:
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**(Sulc1)** P. Sulc, F. Romano, T. E. Ouldridge, et al., J. Chem. Phys. 140, 235102 (2014).
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.. _Sulc02:
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**(Sulc2)** 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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