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Update docs: angle_charmm

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Richard Berger
2019-11-14 15:15:46 -05:00
parent 5d042cf629
commit 9c1d5e76cc
4 changed files with 25 additions and 125 deletions
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doc/src/Eqs/angle_charmm.jpg
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doc/src/Eqs/angle_charmm.tex
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\documentclass[12pt]{article}
\begin{document}
$$
E = K (\theta - \theta_0)^2 + K_{UB} (r - r_{UB})^2
$$
\end{document}

52
doc/src/angle_charmm.rst
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@ -1,22 +1,22 @@
.. index:: angle\_style charmm
.. index:: angle_style charmm
angle\_style charmm command
===========================
angle_style charmm command
==========================
angle\_style charmm/intel command
=================================
angle_style charmm/intel command
================================
angle\_style charmm/kk command
angle_style charmm/kk command
=============================
angle_style charmm/omp command
==============================
angle\_style charmm/omp command
===============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
angle_style charmm
@ -24,7 +24,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
angle_style charmm
angle_coeff 1 300.0 107.0 50.0 3.0
@ -34,12 +34,15 @@ Description
The *charmm* angle style uses the potential
.. image:: Eqs/angle_charmm.jpg
:align: center
.. math::
with an additional Urey\_Bradley term based on the distance *r* between
the 1st and 3rd atoms in the angle. K, theta0, Kub, and Rub are
coefficients defined for each angle type.
E = K (\theta - \theta_0)^2 + K_{ub} (r - r_{ub})^2
with an additional Urey\_Bradley term based on the distance :math:`r` between
the 1st and 3rd atoms in the angle. :math:`K`, :math:`\theta_0`,
:math:`K_{ub}`, and :math:`R_{ub}` are coefficients defined for each angle
type.
See :ref:`(MacKerell) <angle-MacKerell>` for a description of the CHARMM force
field.
@ -49,13 +52,13 @@ The following coefficients must be defined for each angle type via the
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
* K (energy/radian\^2)
* theta0 (degrees)
* K\_ub (energy/distance\^2)
* r\_ub (distance)
* :math:`K` (energy/radian\^2)
* :math:`\theta_0` (degrees)
* :math:`K_{ub}` (energy/distance\^2)
* :math:`r_{ub}` (distance)
Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian\^2.
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of :math:`K` are in energy/radian\^2.
----------
@ -108,8 +111,3 @@ Related commands
**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html