Updated documentation
This commit is contained in:
Oliver Henrich
@ -6,6 +6,9 @@ bond\_style oxdna/fene command
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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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@ -16,6 +19,8 @@ Syntax
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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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@ -28,18 +33,21 @@ Examples
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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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Description
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"""""""""""
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The *oxdna/fene* and *oxdna2/fene* bond styles use the potential
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The *oxdna/fene* , *oxdna2/fene* and *oxrna2/fene* bond styles use the potential
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.. image:: Eqs/bond_oxdna_fene.jpg
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:align: center
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to define a modified finite extensible nonlinear elastic (FENE)
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potential :ref:`(Ouldridge) <oxdna_fene>` to model the connectivity of the
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phosphate backbone in the oxDNA force field for coarse-grained
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modelling of DNA.
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potential :ref:`(Ouldridge) <Ouldridge0>` to model the connectivity of the
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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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@ -55,27 +63,36 @@ commands:
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The oxDNA bond style has to be used together with the
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corresponding oxDNA pair styles for excluded volume interaction
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*oxdna/excv*\ , stacking *oxdna/stk*\ , cross-stacking *oxdna/xstk* and
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*oxdna/excv* , stacking *oxdna/stk* , cross-stacking *oxdna/xstk* and
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coaxial stacking interaction *oxdna/coaxstk* as well as
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hydrogen-bonding interaction *oxdna/hbond* (see also documentation of
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:doc:`pair\_style oxdna/excv <pair_oxdna>`). For the oxDNA2
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:ref:`(Snodin) <oxdna2>` bond style the analogous pair styles and an
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additional Debye-Hueckel pair style *oxdna2/dh* have to be defined.
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:ref:`(Snodin) <Snodin0>` bond style the analogous pair styles
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*oxdna2/excv* , *oxdna2/stk* , *oxdna2/xstk* , *oxdna2/coaxstk* ,
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*oxdna2/hbond* and an additional Debye-Hueckel pair style
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*oxdna2/dh* have to be defined. The same applies to the oxRNA2
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:ref:`(Sulc1) <Sulc01>` styles.
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The coefficients in the above example have to be kept fixed and cannot
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be changed without reparameterizing the entire model.
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Example input and data files for DNA duplexes can be found in
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examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. A simple python
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setup tool which creates single straight or helical DNA strands, DNA
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duplexes or arrays of DNA duplexes can be found in
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Example input and data files for DNA and RNA duplexes can be found in
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examples/USER/cgdna/examples/oxDNA/ , /oxDNA2/ and /oxRNA2/. A simple python
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setup tool which creates single straight or helical DNA strands, DNA/RNA
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duplexes or arrays of DNA/RNA duplexes can be found in
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examples/USER/cgdna/util/.
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Please cite :ref:`(Henrich) <Henrich2>` and the relevant oxDNA articles in
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any publication that uses this implementation. The article contains
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more information on the model, the structure of the input file, the
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setup tool and the performance of the LAMMPS-implementation of oxDNA.
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The preprint version of the article can be found
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Please cite :ref:`(Henrich) <Henrich0>` in any publication that uses
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this implementation. The article 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. The preprint version of the article can be found
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`here <PDF/USER-CGDNA.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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@ -92,35 +109,37 @@ USER-CGDNA package and the MOLECULE and ASPHERE package. See the
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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:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`,
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:doc:`bond\_coeff <bond_coeff>`
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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:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
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**Default:** none
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----------
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.. _Henrich0:
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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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.. _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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**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk,
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T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
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.. _Ouldridge0:
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.. _oxdna\_fene:
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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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**(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye,
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J. Chem. Phys. 134, 085101 (2011).
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.. _Sulc01:
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.. _oxdna2:
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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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**(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al.,
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J. Chem. Phys. 142, 234901 (2015).
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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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.. _lws: http://lammps.sandia.gov
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@ -36,8 +36,8 @@ Syntax
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*oxdna/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 = temperature-independent coefficient in stacking strength
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kappa = coefficient of linear temperature dependence in stacking strength
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xi = 1.3448 (temperature-independent coefficient in stacking strength)
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kappa = 2.6568 (coefficient of linear temperature dependence in stacking strength)
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*oxdna/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 = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs)
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@ -94,11 +94,15 @@ Example input and data files for DNA duplexes can be found in examples/USER/cgdn
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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/USER/cgdna/util/.
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Please cite :ref:`(Henrich) <Henrich1>` and the relevant oxDNA articles in any publication that uses this implementation.
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The article contains more information on the model, the structure of the input file, the setup tool
|
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and the performance of the LAMMPS-implementation of oxDNA.
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The preprint version of the article can be found `here <PDF/USER-CGDNA.pdf>`_.
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Please cite :ref:`(Henrich) <Henrich1>` in any publication that uses
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||||
this implementation. The article contains general information
|
||||
on the model, its implementation and performance as well as the structure of
|
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the data and input file. The preprint version of the article can be found
|
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`here <PDF/USER-CGDNA.pdf>`_.
|
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Please cite also the relevant oxDNA publications
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:ref:`(Ouldridge) <Ouldridge1>`,
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:ref:`(Ouldridge-DPhil) <Ouldridge-DPhil1>`
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and :ref:`(Sulc) <Sulc1>`.
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----------
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@ -114,39 +118,32 @@ USER-CGDNA package and the MOLECULE and ASPHERE package. See the
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Related commands
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""""""""""""""""
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:doc:`bond\_style oxdna/fene <bond_oxdna>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`, :doc:`pair\_coeff <pair_coeff>`,
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:doc:`bond\_style oxdna2/fene <bond_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`
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:doc:`bond\_style oxdna/fene <bond_oxdna>`, :doc:`pair\_coeff <pair_coeff>`,
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:doc:`bond\_style oxdna2/fene <bond_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`,
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:doc:`bond\_style oxrna2/fene <bond_oxdna>`, :doc:`pair\_style oxrna2/excv <pair_oxrna2>`,
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:doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
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**Default:** none
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----------
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.. _Henrich1:
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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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.. _Sulc1:
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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-DPhil1:
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**(Ouldrigde-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
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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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.. _Ouldridge1:
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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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.. _Sulc1:
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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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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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@ -39,15 +39,15 @@ Syntax
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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 = temperature-independent coefficient in stacking strength
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kappa = coefficient of linear temperature dependence in stacking strength
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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 = effective charge (elementary charges)
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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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@ -63,7 +63,7 @@ Examples
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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 1.0 0.815
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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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@ -83,7 +83,7 @@ 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) <Snodin>` and the original oxDNA publications :ref:`(Ouldridge-DPhil) <Ouldridge-DPhil2>`
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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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@ -94,7 +94,7 @@ and :ref:`(Ouldridge) <Ouldridge2>` for a detailed description of the oxDNA2 fo
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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=1.0, qeff=0.815 in the above example). When using a Langevin thermostat
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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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@ -102,11 +102,13 @@ Example input and data files for DNA duplexes can be found in examples/USER/cgdn
|
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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 :ref:`(Henrich) <Henrich>` 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>`_.
|
||||
|
||||
Please cite :ref:`(Henrich) <Henrich2>` in any publication that uses
|
||||
this implementation. The article contains general information
|
||||
on the model, its implementation and performance as well as the structure of
|
||||
the data and input file. The preprint version of the article can be found
|
||||
`here <PDF/USER-CGDNA.pdf>`_.
|
||||
Please cite also the relevant oxDNA2 publications
|
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:ref:`(Snodin) <Snodin2>` and :ref:`(Sulc) <Sulc2>`.
|
||||
|
||||
----------
|
||||
|
||||
@ -122,43 +124,34 @@ USER-CGDNA package and the MOLECULE and ASPHERE package. See the
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`bond\_style oxdna2/fene <bond_oxdna>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`, :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 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:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
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**Default:** none
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----------
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.. _Henrich:
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.. _Henrich2:
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|
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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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.. _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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.. _Snodin:
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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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|
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.. _Ouldridge-DPhil2:
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|
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|
||||
|
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**(Ouldrigde-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
|
||||
**(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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|
||||
|
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|
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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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|
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|
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|
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153
doc/src/pair_oxrna2.rst
Normal file
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doc/src/pair_oxrna2.rst
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.. index:: pair\_style oxrna2/excv
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pair\_style oxrna2/excv command
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===============================
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pair\_style oxrna2/stk command
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==============================
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pair\_style oxrna2/hbond command
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================================
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pair\_style oxrna2/xstk command
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===============================
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pair\_style oxrna2/coaxstk command
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==================================
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pair\_style oxrna2/dh command
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=============================
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Syntax
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""""""
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.. parsed-literal::
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pair_style style1
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pair_coeff \* \* style2 args
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* style1 = *hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh*
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* style2 = *oxrna2/excv* or *oxrna2/stk* or *oxrna2/hbond* or *oxrna2/xstk* or *oxrna2/coaxstk* or *oxrna2/dh*
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* args = list of arguments for these particular styles
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.. parsed-literal::
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*oxrna2/stk* args = seq T xi kappa 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 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 = 1.40206 (temperature-independent coefficient in stacking strength)
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kappa = 2.77 (coefficient of linear temperature dependence in stacking strength)
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*oxrna2/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 = 0.870439 (between base pairs A-T, C-G and G-T) or 0 (all other pairs)
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*oxrna2/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 = 1.02455 (effective charge in elementary charges)
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Examples
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""""""""
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.. parsed-literal::
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pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
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pair_coeff \* \* oxrna2/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 \* \* oxrna2/stk seqdep 0.1 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65
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pair_coeff \* \* oxrna2/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 oxrna2/hbond seqdep 0.870439 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 oxrna2/hbond seqdep 0.870439 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 3 4 oxrna2/hbond seqdep 0.870439 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 \* \* oxrna2/xstk 59.9626 0.5 0.6 0.42 0.58 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68
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pair_coeff \* \* oxrna2/coaxstk 80 0.5 0.6 0.42 0.58 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65
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pair_coeff \* \* oxrna2/dh 0.1 0.5 1.02455
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Description
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"""""""""""
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||||
The *oxrna2* 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 *oxrna2/excv*\ , the stacking *oxrna2/stk*\ , cross-stacking *oxrna2/xstk*
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and coaxial stacking interaction *oxrna2/coaxstk*\ , electrostatic Debye-Hueckel interaction *oxrna2/dh*
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as well as the hydrogen-bonding interaction *oxrna2/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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*oxrna2/fene* for the connectivity of the phosphate backbone (see also documentation of
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:doc:`bond\_style oxrna2/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 *oxrna2/stk* (seq=seqdep, T=0.1, xi=1.40206 and kappa=2.77 in the above example),
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the first coefficient after *oxrna2/hbond* (seq=seqdep in the above example) and the three coefficients
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||||
after *oxrna2/dh* (T=0.1, rhos=0.5, qeff=1.02455 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>`
|
||||
the temperature coefficients have to be matched to the one used in the fix.
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||||
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||||
Example input and data files for DNA duplexes can be found in examples/USER/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/USER/cgdna/util/.
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||||
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||||
Please cite :ref:`(Henrich) <Henrich2>` in any publication that uses
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||||
this implementation. The article contains general information
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||||
on the model, its implementation and performance as well as the structure of
|
||||
the data and input file. The preprint version of the article can be found
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`here <PDF/USER-CGDNA.pdf>`_.
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Please cite also the relevant oxRNA2 publications
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||||
:ref:`(Sulc1) <Sulc31>` and :ref:`(Sulc2) <Sulc32>`.
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||||
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||||
----------
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||||
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Restrictions
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||||
""""""""""""
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||||
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||||
|
||||
These pair styles can only be used if LAMMPS was built with the
|
||||
USER-CGDNA package and the MOLECULE and ASPHERE package. See the
|
||||
:doc:`Build package <Build_package>` doc page for more info.
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||||
|
||||
Related commands
|
||||
""""""""""""""""
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||||
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||||
:doc:`bond\_style oxrna2/fene <bond_oxdna>`, :doc:`pair\_coeff <pair_coeff>`,
|
||||
:doc:`bond\_style oxdna/fene <bond_oxdna>`, :doc:`pair\_style oxdna/excv <pair_oxdna>`,
|
||||
:doc:`bond\_style oxdna2/fene <bond_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`,
|
||||
:doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
----------
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||||
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||||
.. _Henrich3:
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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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||||
|
||||
.. _Sulc31:
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||||
|
||||
**(Sulc1)** P. Sulc, F. Romano, T. E. Ouldridge, et al., J. Chem. Phys. 140, 235102 (2014).
|
||||
|
||||
.. _Sulc32:
|
||||
|
||||
**(Sulc2)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
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||||
.. _lc: Commands_all.html
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||||
Reference in New Issue
Block a user