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Fixed anchor error

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This commit is contained in:
Oliver Henrich
2019-11-15 22:05:12 +00:00
parent 4fa86e6ee8
commit 06c7464a20
2 changed files with 14 additions and 23 deletions
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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) <Davidchack1>`
Apply a rigid-body integrator as described in :ref:`(Davidchack) <Davidchack4>`
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) <Miller1>`.
the quaternion degrees of freedom, similar to the scheme outlined in :ref:`(Miller) <Miller4>`.
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) <Henrich3>`.
Further details of the implementation and stability of the integrator are contained in :ref:`(Henrich) <Henrich4>`.
The preprint version of the article can be found `here <PDF/USER-CGDNA.pdf>`_.
@ -66,19 +66,15 @@ Related commands
----------
.. _Davidchack1:
.. _Miller1:
.. _Davidchack4:
**(Davidchack)** R.L Davidchack, T.E. Ouldridge, and M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
.. _Henrich3:
.. _Miller4:
**(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) <Davidchack2>`
as described in :ref:`(Davidchack) <Davidchack5>`
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) <Miller2>`.
the quaternion norm and is akin to :ref:`(Miller) <Miller5>`.
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) <Dunweg3>`, where a uniform random number is used (instead of
:ref:`(Dunweg) <Dunweg5>`, 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) <Henrich4>`.
Further details of the implementation and stability of the integrators are contained in :ref:`(Henrich) <Henrich5>`.
The preprint version of the article can be found `here <PDF/USER-CGDNA.pdf>`_.
@ -154,24 +154,19 @@ Related commands
----------
.. _Davidchack2:
.. _Miller2:
.. _Davidchack5:
**(Davidchack)** R.L Davidchack, T.E. Ouldridge, M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
.. _Dunweg3:
.. _Miller5:
**(Miller)** T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
.. _Henrich4:
.. _Dunweg5:
**(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).