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Revert "Fixed anchor errors"

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This reverts commit 2d6e84edd7.
This commit is contained in:
Oliver Henrich
2019-11-15 21:59:21 +00:00
parent 2d6e84edd7
commit 4fa86e6ee8
5 changed files with 115 additions and 97 deletions
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75
doc/src/bond_oxdna.rst
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@ -6,6 +6,9 @@ bond\_style oxdna/fene command
bond\_style oxdna2/fene command
===============================
bond\_style oxrna2/fene command
===============================
Syntax
""""""
@ -16,6 +19,8 @@ Syntax
bond_style oxdna2/fene
bond_style oxrna2/fene
Examples
""""""""
@ -28,18 +33,21 @@ Examples
bond_style oxdna2/fene
bond_coeff \* 2.0 0.25 0.7564
bond_style oxrna2/fene
bond_coeff \* 2.0 0.25 0.76107
Description
"""""""""""
The *oxdna/fene* and *oxdna2/fene* bond styles use the potential
The *oxdna/fene* , *oxdna2/fene* and *oxrna2/fene* bond styles use the potential
.. image:: Eqs/bond_oxdna_fene.jpg
:align: center
to define a modified finite extensible nonlinear elastic (FENE)
potential :ref:`(Ouldridge) <oxdna_fene>` to model the connectivity of the
phosphate backbone in the oxDNA force field for coarse-grained
modelling of DNA.
potential :ref:`(Ouldridge) <Ouldridge0>` to model the connectivity of the
phosphate backbone in the oxDNA/oxRNA force field for coarse-grained
modelling of DNA/RNA.
The following coefficients must be defined for the bond type via the
:doc:`bond\_coeff <bond_coeff>` command as given in the above example, or
@ -55,27 +63,36 @@ commands:
The oxDNA bond style has to be used together with the
corresponding oxDNA pair styles for excluded volume interaction
*oxdna/excv*\ , stacking *oxdna/stk*\ , cross-stacking *oxdna/xstk* and
*oxdna/excv* , stacking *oxdna/stk* , cross-stacking *oxdna/xstk* and
coaxial stacking interaction *oxdna/coaxstk* as well as
hydrogen-bonding interaction *oxdna/hbond* (see also documentation of
:doc:`pair\_style oxdna/excv <pair_oxdna>`). For the oxDNA2
:ref:`(Snodin) <oxdna2>` bond style the analogous pair styles and an
additional Debye-Hueckel pair style *oxdna2/dh* have to be defined.
:ref:`(Snodin) <Snodin0>` bond style the analogous pair styles
*oxdna2/excv* , *oxdna2/stk* , *oxdna2/xstk* , *oxdna2/coaxstk* ,
*oxdna2/hbond* and an additional Debye-Hueckel pair style
*oxdna2/dh* have to be defined. The same applies to the oxRNA2
:ref:`(Sulc1) <Sulc01>` styles.
The coefficients in the above example have to be kept fixed and cannot
be changed without reparameterizing the entire model.
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
Example input and data files for DNA and RNA duplexes can be found in
examples/USER/cgdna/examples/oxDNA/ , /oxDNA2/ and /oxRNA2/. A simple python
setup tool which creates single straight or helical DNA strands, DNA/RNA
duplexes or arrays of DNA/RNA duplexes can be found in
examples/USER/cgdna/util/.
Please cite :ref:`(Henrich) <Henrich2>` 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
Please cite :ref:`(Henrich) <Henrich0>` 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 oxDNA/oxRNA publications. These are
:ref:`(Ouldridge) <Ouldridge0>` and
:ref:`(Ouldridge-DPhil) <Ouldridge-DPhil0>` for oxDNA,
:ref:`(Snodin) <Snodin0>` for oxDNA2,
:ref:`(Sulc1) <Sulc01>` for oxRNA2
and for sequence-specific hydrogen-bonding and stacking interactions
:ref:`(Sulc2) <Sulc02>`.
----------
@ -92,35 +109,37 @@ USER-CGDNA package and the MOLECULE and ASPHERE package. See the
Related commands
""""""""""""""""
:doc:`pair\_style oxdna/excv <pair_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`,
:doc:`bond\_coeff <bond_coeff>`
:doc:`pair\_style oxdna/excv <pair_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`, :doc:`pair\_style oxrna2/excv <pair_oxrna2>`,
:doc:`bond\_coeff <bond_coeff>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
**Default:** none
----------
.. _Henrich0:
.. _Henrich2:
**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
.. _Ouldridge-DPhil0:
**(Ouldridge-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk,
T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
.. _Ouldridge0:
.. _oxdna\_fene:
**(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
.. _Snodin0:
**(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
**(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye,
J. Chem. Phys. 134, 085101 (2011).
.. _Sulc01:
.. _oxdna2:
**(Sulc1)** P. Sulc, F. Romano, T. E. Ouldridge, et al., J. Chem. Phys. 140, 235102 (2014).
.. _Sulc02:
**(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al.,
J. Chem. Phys. 142, 234901 (2015).
**(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

16
doc/src/fix_nve_dot.rst
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@ -26,11 +26,11 @@ Examples
Description
"""""""""""
Apply a rigid-body integrator as described in :ref:`(Davidchack) <Davidchack4>`
Apply a rigid-body integrator as described in :ref:`(Davidchack) <Davidchack1>`
to a group of atoms, but without Langevin dynamics.
This command performs Molecular dynamics (MD)
via a velocity-Verlet algorithm and an evolution operator that rotates
the quaternion degrees of freedom, similar to the scheme outlined in :ref:`(Miller) <Miller4>`.
the quaternion degrees of freedom, similar to the scheme outlined in :ref:`(Miller) <Miller1>`.
This command is the equivalent of the :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
without damping and noise and can be used to determine the stability range
@ -40,7 +40,7 @@ The command is equivalent to the :doc:`fix nve <fix_nve>`.
The particles are always considered to have a finite size.
An example input file can be found in /examples/USER/cgdna/examples/duplex1/.
Further details of the implementation and stability of the integrator are contained in :ref:`(Henrich) <Henrich4>`.
Further details of the implementation and stability of the integrator are contained in :ref:`(Henrich) <Henrich3>`.
The preprint version of the article can be found `here <PDF/USER-CGDNA.pdf>`_.
@ -66,15 +66,19 @@ Related commands
----------
.. _Davidchack4:
.. _Davidchack1:
.. _Miller1:
**(Davidchack)** R.L Davidchack, T.E. Ouldridge, and M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
.. _Miller4:
.. _Henrich3:
**(Miller)** T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
.. _Henrich4:
**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).

21
doc/src/fix_nve_dotc_langevin.rst
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@ -38,14 +38,14 @@ Description
"""""""""""
Apply a rigid-body Langevin-type integrator of the kind "Langevin C"
as described in :ref:`(Davidchack) <Davidchack5>`
as described in :ref:`(Davidchack) <Davidchack2>`
to a group of atoms, which models an interaction with an implicit background
solvent. This command performs Brownian dynamics (BD)
via a technique that splits the integration into a deterministic Hamiltonian
part and the Ornstein-Uhlenbeck process for noise and damping.
The quaternion degrees of freedom are updated though an evolution
operator which performs a rotation in quaternion space, preserves
the quaternion norm and is akin to :ref:`(Miller) <Miller5>`.
the quaternion norm and is akin to :ref:`(Miller) <Miller2>`.
In terms of syntax this command has been closely modelled on the
:doc:`fix langevin <fix_langevin>` and its *angmom* option. But it combines
@ -86,7 +86,7 @@ dt damp), where Kb is the Boltzmann constant, T is the desired
temperature, m is the mass of the particle, dt is the timestep size,
and damp is the damping factor. Random numbers are used to randomize
the direction and magnitude of this force as described in
:ref:`(Dunweg) <Dunweg5>`, where a uniform random number is used (instead of
:ref:`(Dunweg) <Dunweg3>`, where a uniform random number is used (instead of
a Gaussian random number) for speed.
@ -128,7 +128,7 @@ The scale factor after the *angmom* keyword gives the ratio of the rotational to
the translational friction coefficient.
An example input file can be found in /examples/USER/cgdna/examples/duplex2/.
Further details of the implementation and stability of the integrators are contained in :ref:`(Henrich) <Henrich5>`.
Further details of the implementation and stability of the integrators are contained in :ref:`(Henrich) <Henrich4>`.
The preprint version of the article can be found `here <PDF/USER-CGDNA.pdf>`_.
@ -154,19 +154,24 @@ Related commands
----------
.. _Davidchack5:
.. _Davidchack2:
.. _Miller2:
**(Davidchack)** R.L Davidchack, T.E. Ouldridge, M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
.. _Miller5:
.. _Dunweg3:
**(Miller)** T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
.. _Dunweg5:
.. _Henrich4:
**(Dunweg)** B. Dunweg, W. Paul, Int. J. Mod. Phys. C, 2, 817-27 (1991).
.. _Henrich5:
**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).

45
doc/src/pair_oxdna.rst
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@ -36,8 +36,8 @@ Syntax
*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
seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
T = temperature (oxDNA units, 0.1 = 300 K)
xi = temperature-independent coefficient in stacking strength
kappa = coefficient of linear temperature dependence in stacking strength
xi = 1.3448 (temperature-independent coefficient in stacking strength)
kappa = 2.6568 (coefficient of linear temperature dependence in stacking strength)
*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
seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs)
@ -94,11 +94,15 @@ Example input and data files for DNA duplexes can be found in examples/USER/cgdn
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) <Henrich1>` 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) <Henrich1>` 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 oxDNA publications
:ref:`(Ouldridge) <Ouldridge1>`,
:ref:`(Ouldridge-DPhil) <Ouldridge-DPhil1>`
and :ref:`(Sulc) <Sulc1>`.
----------
@ -114,39 +118,32 @@ USER-CGDNA package and the MOLECULE and ASPHERE package. See the
Related commands
""""""""""""""""
:doc:`bond\_style oxdna/fene <bond_oxdna>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`, :doc:`pair\_coeff <pair_coeff>`,
:doc:`bond\_style oxdna2/fene <bond_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`
:doc:`bond\_style oxdna/fene <bond_oxdna>`, :doc:`pair\_coeff <pair_coeff>`,
:doc:`bond\_style oxdna2/fene <bond_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`,
:doc:`bond\_style oxrna2/fene <bond_oxdna>`, :doc:`pair\_style oxrna2/excv <pair_oxrna2>`,
:doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
**Default:** none
----------
.. _Henrich1:
**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
.. _Sulc1:
**(Sulc)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
.. _Ouldridge-DPhil1:
**(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).
.. _Ouldridge1:
**(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
.. _Sulc1:
**(Sulc)** 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

55
doc/src/pair_oxdna2.rst
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@ -39,15 +39,15 @@ Syntax
*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
seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
T = temperature (oxDNA units, 0.1 = 300 K)
xi = temperature-independent coefficient in stacking strength
kappa = coefficient of linear temperature dependence in stacking strength
xi = 1.3523 (temperature-independent coefficient in stacking strength)
kappa = 2.6717 (coefficient of linear temperature dependence in stacking strength)
*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
seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
eps = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs)
*oxdna2/dh* args = T rhos qeff
T = temperature (oxDNA units, 0.1 = 300 K)
rhos = salt concentration (mole per litre)
qeff = effective charge (elementary charges)
qeff = 0.815 (effective charge in elementary charges)
Examples
""""""""
@ -63,7 +63,7 @@ Examples
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
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
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
pair_coeff \* \* oxdna2/dh 0.1 1.0 0.815
pair_coeff \* \* oxdna2/dh 0.1 0.5 0.815
Description
"""""""""""
@ -83,7 +83,7 @@ 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) <Snodin>` and the original oxDNA publications :ref:`(Ouldridge-DPhil) <Ouldridge-DPhil2>`
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::
@ -94,7 +94,7 @@ and :ref:`(Ouldridge) <Ouldridge2>` for a detailed description of the oxDNA2 fo
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 *oxdna2/stk* (seq=seqdep, T=0.1, xi=1.3523 and kappa=2.6717 in the above example),
the first coefficient after *oxdna2/hbond* (seq=seqdep in the above example) and the three coefficients
after *oxdna2/dh* (T=0.1, rhos=1.0, qeff=0.815 in the above example). When using a Langevin thermostat
after *oxdna2/dh* (T=0.1, rhos=0.5, qeff=0.815 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.
@ -102,11 +102,13 @@ Example input and data files for DNA duplexes can be found in examples/USER/cgdn
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
: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>`,
:doc:`bond\_style oxdna/fene <bond_oxdna>`, :doc:`pair\_style oxdna/excv <pair_oxdna>`
:doc:`bond\_style oxdna2/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 oxrna2/fene <bond_oxdna>`, :doc:`pair\_style oxrna2/excv <pair_oxrna2>`,
:doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
**Default:** none
----------
.. _Henrich:
.. _Henrich2:
**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
.. _Sulc2:
**(Sulc)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
.. _Snodin:
.. _Snodin2:
**(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
.. _Sulc2:
**(Sulc)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
.. _Ouldridge-DPhil2:
**(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).
.. _Ouldridge2:
**(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).