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14
doc/html/_sources/Section_howto.txt
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@ -221,7 +221,7 @@ commands like :doc:`pair_coeff <pair_coeff>` or
for additional tools that can use CHARMM or AMBER to assign force
field coefficients and convert their output into LAMMPS input.
See :ref:`(MacKerell) <MacKerell>` for a description of the CHARMM force
See :ref:`(MacKerell) <howto-MacKerell>` for a description of the CHARMM force
field. See :ref:`(Cornell) <Cornell>` for a description of the AMBER force
field.
@ -507,7 +507,7 @@ TIP3P water model
-----------------
The TIP3P water model as implemented in CHARMM
:ref:`(MacKerell) <MacKerell>` specifies a 3-site rigid water molecule with
:ref:`(MacKerell) <howto-MacKerell>` specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
In LAMMPS the :doc:`fix shake <fix_shake>` command can be used to hold
the two O-H bonds and the H-O-H angle rigid. A bond style of
@ -706,7 +706,7 @@ the partial charge assignemnts change:
| H charge = 0.4238
|
See the :ref:`(Berendsen) <Berendsen>` reference for more details on both
See the :ref:`(Berendsen) <howto-Berendsen>` reference for more details on both
the SPC and SPC/E models.
Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_.
@ -2978,7 +2978,7 @@ The thermalized Drude model, similarly to the :ref:`core-shell <howto_26>`
model, representes induced dipoles by a pair of charges (the core atom
and the Drude particle) connected by a harmonic spring. The Drude
model has a number of features aimed at its use in molecular systems
(:ref:`Lamoureux and Roux <Lamoureux>`):
(:ref:`Lamoureux and Roux <howto-Lamoureux>`):
* Thermostating of the additional degrees of freedom associated with the
induced dipoles at very low temperature, in terms of the reduced
@ -3030,7 +3030,7 @@ too close, which can cause numerical issues.
.. _Berendsen:
.. _howto-Berendsen:
@ -3058,7 +3058,7 @@ J Chem Phys, 120, 9665 (2004).
**(Ikeshoji)** Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261
(1994).
.. _MacKerell:
.. _howto-MacKerell:
@ -3098,7 +3098,7 @@ Phys, 79, 926 (1983).
**(Mitchell and Finchham)** Mitchell, Finchham, J Phys Condensed Matter,
5, 1031-1038 (1993).
.. _Lamoureux:
.. _howto-Lamoureux:

4
doc/html/_sources/bond_fene.txt
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@ -33,7 +33,7 @@ The *fene* bond style uses the potential
:align: center
to define a finite extensible nonlinear elastic (FENE) potential
:ref:`(Kremer) <Kremer>`, used for bead-spring polymer models. The first
:ref:`(Kremer) <fene-Kremer>`, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive. The
first term extends to R0, the maximum extent of the bond. The 2nd
term is cutoff at 2^(1/6) sigma, the minimum of the LJ potential.
@ -97,7 +97,7 @@ Related commands
----------
.. _Kremer:
.. _fene-Kremer:

4
doc/html/_sources/compute_xrd.txt
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@ -52,7 +52,7 @@ Description
"""""""""""
Define a computation that calculates x-ray diffraction intensity as described
in :ref:`(Coleman) <Coleman>` on a mesh of reciprocal lattice nodes defined
in :ref:`(Coleman) <xrd-Coleman>` on a mesh of reciprocal lattice nodes defined
by the entire simulation domain (or manually) using a simulated radiation
of wavelength lambda.
@ -209,7 +209,7 @@ no manual flag, no echo flag.
----------
.. _Coleman:
.. _xrd-Coleman:

11
doc/html/_sources/dihedral_charmm.txt
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@ -35,10 +35,11 @@ The *charmm* dihedral style uses the potential
.. image:: Eqs/dihedral_charmm.jpg
:align: center
See :ref:`(MacKerell) <dihedral-MacKerell>` for a description of the CHARMM force
field. This dihedral style can also be used for the AMBER force field
(see comment on weighting factors below). See :ref:`(Cornell) <Cornell>`
for a description of the AMBER force field.
See :ref:`(MacKerell) <dihedral-MacKerell>` for a description of the CHARMM
force field. This dihedral style can also be used for the AMBER force
field (see comment on weighting factors below). See
:ref:`(Cornell) <dihedral-Cornell>` for a description of the AMBER force
field.
The following coefficients must be defined for each dihedral type via the
:doc:`dihedral_coeff <dihedral_coeff>` command as in the example above, or in
@ -121,7 +122,7 @@ Related commands
----------
.. _Cornell:
.. _dihedral-Cornell:

20
doc/html/_sources/fix_nh.txt
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@ -122,12 +122,12 @@ particles will match the target values specified by Tstart/Tstop and
Pstart/Pstop.
The equations of motion used are those of Shinoda et al in
:ref:`(Shinoda) <Shinoda>`, which combine the hydrostatic equations of
Martyna, Tobias and Klein in :ref:`(Martyna) <Martyna>` with the strain
:ref:`(Shinoda) <nh-Shinoda>`, which combine the hydrostatic equations of
Martyna, Tobias and Klein in :ref:`(Martyna) <nh-Martyna>` with the strain
energy proposed by Parrinello and Rahman in
:ref:`(Parrinello) <Parrinello>`. The time integration schemes closely
:ref:`(Parrinello) <nh-Parrinello>`. The time integration schemes closely
follow the time-reversible measure-preserving Verlet and rRESPA
integrators derived by Tuckerman et al in :ref:`(Tuckerman) <Tuckerman>`.
integrators derived by Tuckerman et al in :ref:`(Tuckerman) <nh-Tuckerman>`.
----------
@ -320,7 +320,7 @@ barostat variables.
The *mtk* keyword controls whether or not the correction terms due to
Martyna, Tuckerman, and Klein are included in the equations of motion
:ref:`(Martyna) <Martyna>`. Specifying *no* reproduces the original
:ref:`(Martyna) <nh-Martyna>`. Specifying *no* reproduces the original
Hoover barostat, whose volume probability distribution function
differs from the true NPT and NPH ensembles by a factor of 1/V. Hence
using *yes* is more correct, but in many cases the difference is
@ -330,7 +330,7 @@ The keyword *tloop* can be used to improve the accuracy of integration
scheme at little extra cost. The initial and final updates of the
thermostat variables are broken up into *tloop* substeps, each of
length *dt*\ /\ *tloop*\ . This corresponds to using a first-order
Suzuki-Yoshida scheme :ref:`(Tuckerman) <Tuckerman>`. The keyword *ploop*
Suzuki-Yoshida scheme :ref:`(Tuckerman) <nh-Tuckerman>`. The keyword *ploop*
does the same thing for the barostat thermostat.
The keyword *nreset* controls how often the reference dimensions used
@ -698,26 +698,26 @@ not coupled to barostat, otherwise no.
----------
.. _Martyna:
.. _nh-Martyna:
**(Martyna)** Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).
.. _Parrinello:
.. _nh-Parrinello:
**(Parrinello)** Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).
.. _Tuckerman:
.. _nh-Tuckerman:
**(Tuckerman)** Tuckerman, Alejandre, Lopez-Rendon, Jochim, and
Martyna, J Phys A: Math Gen, 39, 5629 (2006).
.. _Shinoda:
.. _nh-Shinoda: