forked from lijiext/lammps
Updated documentation
This commit is contained in:
Oliver Henrich
parent
bac8d15764
commit
1df3a71734
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@ -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
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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 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,
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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) <Henrich>` 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) <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
|
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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 oxDNA2 publications
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:ref:`(Snodin) <Snodin2>` and :ref:`(Sulc) <Sulc2>`.
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----------
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@ -122,43 +124,34 @@ 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 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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**(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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.. _Ouldridge-DPhil2:
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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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.. _Ouldridge2:
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||||
|
||||
|
||||
|
||||
**(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,153 @@
|
|||
.. index:: pair\_style oxrna2/excv
|
||||
|
||||
pair\_style oxrna2/excv command
|
||||
===============================
|
||||
|
||||
pair\_style oxrna2/stk command
|
||||
==============================
|
||||
|
||||
pair\_style oxrna2/hbond command
|
||||
================================
|
||||
|
||||
pair\_style oxrna2/xstk command
|
||||
===============================
|
||||
|
||||
pair\_style oxrna2/coaxstk command
|
||||
==================================
|
||||
|
||||
pair\_style oxrna2/dh command
|
||||
=============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
pair_style style1
|
||||
|
||||
pair_coeff \* \* style2 args
|
||||
|
||||
* style1 = *hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh*
|
||||
|
||||
* style2 = *oxrna2/excv* or *oxrna2/stk* or *oxrna2/hbond* or *oxrna2/xstk* or *oxrna2/coaxstk* or *oxrna2/dh*
|
||||
* args = list of arguments for these particular styles
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*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
|
||||
seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
|
||||
T = temperature (oxDNA units, 0.1 = 300 K)
|
||||
xi = 1.40206 (temperature-independent coefficient in stacking strength)
|
||||
kappa = 2.77 (coefficient of linear temperature dependence in stacking strength)
|
||||
*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
|
||||
seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
|
||||
eps = 0.870439 (between base pairs A-T, C-G and G-T) or 0 (all other pairs)
|
||||
*oxrna2/dh* args = T rhos qeff
|
||||
T = temperature (oxDNA units, 0.1 = 300 K)
|
||||
rhos = salt concentration (mole per litre)
|
||||
qeff = 1.02455 (effective charge in elementary charges)
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
|
||||
pair_coeff \* \* oxrna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
pair_coeff \* \* oxrna2/dh 0.1 0.5 1.02455
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *oxrna2* pair styles compute the pairwise-additive parts of the oxDNA force field
|
||||
for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
|
||||
excluded volume interaction *oxrna2/excv*\ , the stacking *oxrna2/stk*\ , cross-stacking *oxrna2/xstk*
|
||||
and coaxial stacking interaction *oxrna2/coaxstk*\ , electrostatic Debye-Hueckel interaction *oxrna2/dh*
|
||||
as well as the hydrogen-bonding interaction *oxrna2/hbond* between complementary pairs of nucleotides on
|
||||
opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
|
||||
are supported :ref:`(Sulc) <Sulc2>`. Quasi-unique base-pairing between nucleotides can be achieved by using
|
||||
more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc.
|
||||
This prevents the hybridization of in principle complementary bases within Ntypes/4 bases
|
||||
up and down along the backbone.
|
||||
|
||||
The exact functional form of the pair styles is rather complex.
|
||||
The individual potentials consist of products of modulation factors,
|
||||
which themselves are constructed from a number of more basic potentials
|
||||
(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
|
||||
We refer to :ref:`(Snodin) <Snodin2>` and the original oxDNA publications :ref:`(Ouldridge-DPhil) <Ouldridge-DPhil2>`
|
||||
and :ref:`(Ouldridge) <Ouldridge2>` for a detailed description of the oxDNA2 force field.
|
||||
|
||||
.. note::
|
||||
|
||||
These pair styles have to be used together with the related oxDNA2 bond style
|
||||
*oxrna2/fene* for the connectivity of the phosphate backbone (see also documentation of
|
||||
:doc:`bond\_style oxrna2/fene <bond_oxdna>`). Most of the coefficients
|
||||
in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
|
||||
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),
|
||||
the first coefficient after *oxrna2/hbond* (seq=seqdep in the above example) and the three coefficients
|
||||
after *oxrna2/dh* (T=0.1, rhos=0.5, qeff=1.02455 in the above example). When using a Langevin thermostat
|
||||
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.
|
||||
|
||||
Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
|
||||
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) <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 oxRNA2 publications
|
||||
:ref:`(Sulc1) <Sulc31>` and :ref:`(Sulc2) <Sulc32>`.
|
||||
|
||||
----------
|
||||
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
|
||||
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.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
: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
|
||||
|
||||
|
||||
----------
|
||||
|
||||
.. _Henrich3:
|
||||
|
||||
**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
|
||||
|
||||
.. _Sulc31:
|
||||
|
||||
**(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
|
||||
.. _lc: Commands_all.html
|
||||
|
|
@ -1,8 +1,12 @@
|
|||
This directory contains example data and input files
|
||||
and utility scripts for the oxDNA coarse-grained model
|
||||
for DNA.
|
||||
as well as utility scripts for the oxDNA/oxDNA2/oxRNA2
|
||||
coarse-grained model for DNA and RNA.
|
||||
|
||||
/******************************************************************************/
|
||||
|
||||
/examples/oxDNA/duplex1:
|
||||
/examples/oxDNA2/duplex1:
|
||||
|
||||
/examples/duplex1:
|
||||
Input, data and log files for a DNA duplex (double-stranded DNA)
|
||||
consisiting of 5 base pairs. The duplex contains two strands with
|
||||
complementary base pairs. The topology is
|
||||
|
|
@ -11,7 +15,14 @@ A - C - G - T - A
|
|||
| | | | |
|
||||
T - G - C - A - T
|
||||
|
||||
/examples/duplex2:
|
||||
Note that in this example the stacking and hydrogen-bonding interactions
|
||||
are sequence-averaged (cf. keyword 'seqav' in according pair styles).
|
||||
|
||||
/******************************************************************************/
|
||||
|
||||
/examples/oxDNA/duplex2:
|
||||
/examples/oxDNA2/duplex2:
|
||||
|
||||
Input, data and log files for a nicked DNA duplex (double-stranded DNA)
|
||||
consisiting of 8 base pairs. The duplex contains strands with
|
||||
complementary base pairs, but the backbone on one side is not continuous:
|
||||
|
|
@ -22,9 +33,15 @@ A - C - G - T - A - C - G - T
|
|||
| | | | | | | |
|
||||
T - G - C - A T - G - C - A
|
||||
|
||||
/examples/duplex3:
|
||||
This is basically the duplex1 run with sequence-dependent stacking
|
||||
and hydrogen-bonding strengths enabled and both nucleotide mass and
|
||||
Note that in this example the stacking and hydrogen-bonding interactions
|
||||
are sequence-averaged (cf. keyword 'seqav' in according pair styles).
|
||||
|
||||
/******************************************************************************/
|
||||
|
||||
/examples/oxDNA2/duplex3:
|
||||
|
||||
This is the duplex1 run with sequence-dependent stacking and
|
||||
hydrogen-bonding strengths enabled and both nucleotide mass and
|
||||
moment of inertia set to the value of the standalone implementation
|
||||
of oxDNA (M = I = 1). To achieve this, the masses can be set directly
|
||||
in the input and data file, whereas the moment of inertia is set via
|
||||
|
|
@ -33,6 +50,19 @@ The change of mass and moment of inertia allows direct comparision of
|
|||
e.g. trajectory data, energies or time-dependent observables on a per-timestep
|
||||
basis until numerical noise causes deviations at later simulation times.
|
||||
|
||||
As mentioned above, the stacking and hydrogen-bonding interactions
|
||||
are sequence-dependent (cf. keyword 'seqdep' in according pair styles).
|
||||
|
||||
/******************************************************************************/
|
||||
|
||||
/examples/oxRNA2/duplex4
|
||||
|
||||
This is the duplex2 run with the oxRNA2 force field instead of the oxDNA or
|
||||
oxDNA2 force field and sequence-dependent stacking and hydrogen-bonding
|
||||
strengths enabled.
|
||||
|
||||
/******************************************************************************/
|
||||
|
||||
/util:
|
||||
This directory contains a simple python setup tool which creates
|
||||
single straight or helical DNA strands, DNA duplexes or arrays of DNA
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
variable number equal 1
|
||||
variable number equal 3
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 0.1
|
||||
|
|
|
|||
|
|
@ -1,5 +1,5 @@
|
|||
LAMMPS (7 Aug 2019)
|
||||
variable number equal 1
|
||||
variable number equal 3
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 0.1
|
||||
|
|
|
|||
|
|
@ -1,5 +1,5 @@
|
|||
LAMMPS (7 Aug 2019)
|
||||
variable number equal 1
|
||||
variable number equal 3
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 0.1
|
||||
|
|
|
|||
|
|
@ -0,0 +1,96 @@
|
|||
# LAMMPS data file
|
||||
16 atoms
|
||||
16 ellipsoids
|
||||
13 bonds
|
||||
|
||||
4 atom types
|
||||
1 bond types
|
||||
|
||||
# System size
|
||||
-20.000000 20.000000 xlo xhi
|
||||
-20.000000 20.000000 ylo yhi
|
||||
-20.000000 20.000000 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 3.1575
|
||||
2 3.1575
|
||||
3 3.1575
|
||||
4 3.1575
|
||||
|
||||
# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
|
||||
Atoms
|
||||
|
||||
1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1
|
||||
2 2 -4.860249842674776e-01 -3.518234140414736e-01 3.897628551303122e-01 1 1 1
|
||||
3 3 -1.874009511073395e-01 -5.699832309147915e-01 7.795257102606244e-01 1 1 1
|
||||
4 4 1.824198365552941e-01 -5.715968887521518e-01 1.169288565390937e+00 1 1 1
|
||||
5 1 4.829362784135484e-01 -3.560513319622209e-01 1.559051420521249e+00 1 1 1
|
||||
6 2 5.999771538385027e-01 -5.235921299024461e-03 1.948814275651561e+00 1 1 1
|
||||
7 3 4.890766774371325e-01 3.475687034056071e-01 2.338577130781873e+00 1 1 1
|
||||
8 4 1.923677943514057e-01 5.683261666476170e-01 2.728339985912185e+00 1 1 1
|
||||
9 1 -1.923677943514057e-01 -5.683261666476170e-01 2.728339985912185e+00 2 1 1
|
||||
10 2 -4.890766774371324e-01 -3.475687034056071e-01 2.338577130781873e+00 2 1 1
|
||||
11 3 -5.999771538385025e-01 5.235921299024461e-03 1.948814275651561e+00 2 1 1
|
||||
12 4 -4.829362784135481e-01 3.560513319622207e-01 1.559051420521249e+00 2 1 1
|
||||
13 1 -1.824198365552940e-01 5.715968887521514e-01 1.169288565390936e+00 2 1 1
|
||||
14 2 1.874009511073395e-01 5.699832309147912e-01 7.795257102606241e-01 2 1 1
|
||||
15 3 4.860249842674773e-01 3.518234140414733e-01 3.897628551303119e-01 2 1 1
|
||||
16 4 5.999999999999995e-01 -3.330669073875470e-17 -3.330669073875470e-16 2 1 1
|
||||
|
||||
# Atom-ID, translational velocity, angular momentum
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
11 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
12 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
13 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
14 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
15 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
16 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
|
||||
# Atom-ID, shape, quaternion
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.513258223252946e-01 0.000000000000000e+00 0.000000000000000e+00 3.081869234362515e-01
|
||||
3 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 8.100416404457962e-01 0.000000000000000e+00 0.000000000000000e+00 5.863723567357894e-01
|
||||
4 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.899012371043606e-01 0.000000000000000e+00 0.000000000000000e+00 8.074754054847398e-01
|
||||
5 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 3.123349185122326e-01 0.000000000000000e+00 0.000000000000000e+00 9.499720515246527e-01
|
||||
6 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 4.363309284746654e-03 0.000000000000000e+00 0.000000000000000e+00 9.999904807207346e-01
|
||||
7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -3.040330609254902e-01 0.000000000000000e+00 0.000000000000000e+00 9.526614812535865e-01
|
||||
8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.828323126827837e-01 0.000000000000000e+00 0.000000000000000e+00 -8.125924533816677e-01
|
||||
9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.125924533816681e-01 5.828323126827832e-01 -0.000000000000000e+00
|
||||
10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.526614812535864e-01 3.040330609254902e-01 0.000000000000000e+00
|
||||
11 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.999904807207346e-01 -4.363309284746654e-03 0.000000000000000e+00
|
||||
12 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.499720515246526e-01 -3.123349185122325e-01 0.000000000000000e+00
|
||||
13 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.074754054847402e-01 -5.899012371043603e-01 0.000000000000000e+00
|
||||
14 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.863723567357898e-01 -8.100416404457959e-01 0.000000000000000e+00
|
||||
15 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -3.081869234362514e-01 9.513258223252948e-01 0.000000000000000e+00
|
||||
16 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 2.775557561562893e-17 1.000000000000000e+00 -0.000000000000000e+00
|
||||
|
||||
# Bond topology
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 9 10
|
||||
9 1 10 11
|
||||
10 1 11 12
|
||||
11 1 13 14
|
||||
12 1 14 15
|
||||
13 1 15 16
|
||||
|
|
@ -0,0 +1,80 @@
|
|||
variable number equal 4
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 0.1
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex4
|
||||
|
||||
set atom * mass 3.1575
|
||||
|
||||
group all type 1 4
|
||||
|
||||
# oxRNA2 bond interactions - FENE backbone
|
||||
bond_style oxrna2/fene
|
||||
bond_coeff * 2.0 0.25 0.761070781051
|
||||
|
||||
# oxRNA2 pair interactions
|
||||
pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
|
||||
|
||||
pair_coeff * * oxrna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxrna2/stk seqdep ${T} 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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
pair_coeff * * oxrna2/dh ${T} 0.5 1.02455
|
||||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/dot
|
||||
fix 1 all nve/asphere
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f"
|
||||
|
||||
run 1000000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
Loading…
Reference in New Issue