remove more `\_` escapes from doc anchors and a bunch of other issues found in the process

* water potentials: TIP3P, TIP4P, SPC

* implicit solvent potentials: hydrodynamic lubrication, Debye

* force-field compatibility with common CHARMM, AMBER, DREIDING,     OPLS, GROMACS, COMPASS options

* access to the `OpenKIM Repository <http://openkim.org>`_ of potentials via     :doc:`kim\_init, kim\_interactions, and kim\_query <kim_commands>` commands

* access to the `OpenKIM Repository <http://openkim.org>`_ of potentials via     :doc:`kim_init, kim_interactions, and kim_query <kim_commands>` commands

* hybrid potentials: multiple pair, bond, angle, dihedral, improper     potentials can be used in one simulation

* overlaid potentials: superposition of multiple pair potentials

* src/RIGID: filenames -> commands

* :doc:`compute erotate/rigid <compute_erotate_rigid>`

* fix shake"_fix\_shake.html

* :doc:`fix shake <fix_shake>`

* :doc:`fix rattle <fix_shake>`

* :doc:`fix rigid/\* <fix_rigid>`

* examples/ASPHERE

decorrelation time.

HMA should not be used if atoms are expected to diffuse.  It is also

restricted to simulations in the NVT ensemble.  While this compute may be

used with any potential in LAMMPS, it will provide inaccurate results

restricted to simulations in the NVT ensemble.  While this compute may

be used with any potential in LAMMPS, it will provide inaccurate results

for potentials that do not go to 0 at the truncation distance;

:doc:`pair\_lj\_smooth\_linear <pair_lj_smooth_linear>` and Ewald summation should

work fine, while :doc:`pair_lj <pair_lj>` will perform poorly unless

the potential is shifted (via :doc:`pair_modify <pair_modify>` shift) or the cutoff is large.  Furthermore, computation of the heat capacity with

this compute is restricted to those that implement the single\_hessian method

in Pair.  Implementing single\_hessian in additional pair styles is simple.

Please contact Andrew Schultz (ajs42 at buffalo.edu) and David Kofke (kofke at

buffalo.edu) if your desired pair style does not have this method.  This is

the list of pair styles that currently implement pair\_hessian:

* :doc:`lj\_smooth\_linear <pair_lj_smooth_linear>`

:doc:`pair_style lj/smooth/linear <pair_lj_smooth_linear>` and Ewald

summation should work fine, while :doc:`pair_style lj/cut <pair_lj>`

will perform poorly unless the potential is shifted (via

:doc:`pair_modify <pair_modify>` shift) or the cutoff is large.

Furthermore, computation of the heat capacity with this compute is

restricted to those that implement the *single\_hessian* method in Pair.

Implementing *single\_hessian* in additional pair styles is simple.

Please contact Andrew Schultz (ajs42 at buffalo.edu) and David Kofke

(kofke at buffalo.edu) if your desired pair style does not have this

method.  This is the list of pair styles that currently implement

*single\_hessian*:

* :doc:`pair_style lj/smooth/linear <pair_lj_smooth_linear>`

In this method, the analytically known harmonic behavior of a crystal is removed from the traditional ensemble

""""""""""""""""

:doc:`dihedral_coeff <dihedral_coeff>`,

:doc:`angle\_cosine\_shift\_exp <angle_cosine_shift_exp>`

:doc:`angle_style cosine/shift/exp <angle_cosine_shift_exp>`

**Default:** none

Related commands

""""""""""""""""

:doc:`compute fep <compute_fep>`, :doc:`fix adapt <fix_adapt>`, :doc:`compute ti <compute_ti>`, :doc:`pair\_fep\_soft <pair_fep_soft>`

:doc:`compute fep <compute_fep>`, :doc:`fix adapt <fix_adapt>`, :doc:`compute ti <compute_ti>`, :doc:`pair_style \*/soft <pair_fep_soft>`

Default

"""""""