166 lines
7.8 KiB
ReStructuredText
166 lines
7.8 KiB
ReStructuredText
.. index:: pair_style oxdna2/excv
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.. index:: pair_style oxdna2/stk
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.. index:: pair_style oxdna2/hbond
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.. index:: pair_style oxdna2/xstk
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.. index:: pair_style oxdna2/coaxstk
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.. index:: pair_style oxdna2/dh
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pair_style oxdna2/excv command
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==============================
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pair_style oxdna2/stk command
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=============================
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pair_style oxdna2/hbond command
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===============================
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pair_style oxdna2/xstk command
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==============================
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pair_style oxdna2/coaxstk command
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=================================
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pair_style oxdna2/dh 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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pair_style style1
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pair_coeff * * style2 args
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* style1 = *hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh*
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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
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.. parsed-literal::
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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 = 1.3523 (temperature-independent coefficient in stacking strength)
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kappa = 2.6717 (coefficient of linear temperature dependence in stacking strength)
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*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
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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 = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs)
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*oxdna2/dh* args = T rhos qeff
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T = temperature (oxDNA units, 0.1 = 300 K)
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rhos = salt concentration (mole per litre)
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qeff = 0.815 (effective charge in elementary charges)
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Examples
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""""""""
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.. code-block:: LAMMPS
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pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
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pair_coeff * * oxdna2/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 * * 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
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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
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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
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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
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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
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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
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pair_coeff * * oxdna2/dh 0.1 0.5 0.815
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Description
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"""""""""""
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The *oxdna2* 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 *oxdna2/excv*, the stacking *oxdna2/stk*, cross-stacking *oxdna2/xstk*
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and coaxial stacking interaction *oxdna2/coaxstk*, electrostatic Debye-Hueckel interaction *oxdna2/dh*
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as well as the hydrogen-bonding interaction *oxdna2/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 :ref:`(Sulc) <Sulc2>`. 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 :ref:`(Snodin) <Snodin2>` and the original oxDNA publications :ref:`(Ouldridge-DPhil) <Ouldridge-DPhil2>`
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and :ref:`(Ouldridge) <Ouldridge2>` for a detailed description of the oxDNA2 force field.
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.. note::
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These pair styles have to be used together with the related oxDNA2 bond style
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*oxdna2/fene* for the connectivity of the phosphate backbone (see also documentation of
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:doc:`bond_style oxdna2/fene <bond_oxdna>`). 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 *oxdna2/stk* (seq=seqdep, T=0.1, xi=1.3523 and kappa=2.6717 in the above example),
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the first coefficient after *oxdna2/hbond* (seq=seqdep in the above example) and the three coefficients
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after *oxdna2/dh* (T=0.1, rhos=0.5, qeff=0.815 in the above example). When using a Langevin thermostat
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e.g. through :doc:`fix langevin <fix_langevin>` or :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
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the temperature coefficients have to be matched to the one used in the fix.
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.. note::
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These pair styles have to be used with the *atom_style hybrid bond ellipsoid oxdna*
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(see documentation of :doc:`atom_style <atom_style>`). The *atom_style oxdna*
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stores the 3'-to-5' polarity of the nucleotide strand, which is set through
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the bond topology in the data file. The first (second) atom in a bond definition
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is understood to point towards the 3'-end (5'-end) of the strand.
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Example input and data files for DNA duplexes can be found in examples/PACKAGES/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/PACKAGES/cgdna/util/.
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Please cite :ref:`(Henrich) <Henrich2>` 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 oxDNA2 publications
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:ref:`(Snodin) <Snodin2>` and :ref:`(Sulc) <Sulc2>`.
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----------
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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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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:`bond_style oxdna2/fene <bond_oxdna>`, :doc:`pair_coeff <pair_coeff>`,
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:doc:`bond_style oxdna/fene <bond_oxdna>`, :doc:`pair_style oxdna/excv <pair_oxdna>`,
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:doc:`bond_style oxrna2/fene <bond_oxdna>`, :doc:`pair_style oxrna2/excv <pair_oxrna2>`,
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: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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.. _Henrich2:
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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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.. _Snodin2:
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**(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
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.. _Sulc2:
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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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.. _Ouldridge-DPhil2:
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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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.. _Ouldridge2:
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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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