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improve OPLS description

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Axel Kohlmeyer
2024-10-18 21:51:43 -04:00
parent 2074b0c400
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doc/src/Howto_bioFF.rst
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@ -236,26 +236,33 @@ documentation for the formula it computes.
* :doc:`special_bonds <special_bonds>` dreiding
OPLS-AA
-------
OPLS
----
OPLS-AA is a general force field for atomistic simulation of proteins in
their native environment, developed at the `Jorgensen group
OPLS (Optimized Potentials for Liquid Simulations) is a general force
field for atomistic simulation of organic molecules in solvent. It was
developed at the `Jorgensen group
<https://traken.chem.yale.edu/oplsaam.html>`_ at Purdue University and
later at Yale University.
later at Yale University. Multiple versions of the OPLS parameters
exist for united atom representations (OPLS-UA) and for all-atom
representations (OPLS-AA).
This force field is based on atom types mapping to specific functional
groups in organic and biological molecules. The atom type includes an
average atomic charge reflecting the oxidation state of the element in a
specific chemical bond :ref:`(Jorgensen) <howto-jorgensen>`.
specific chemical bond :ref:`(Jorgensen) <howto-jorgensen>` and computed
based on increments determined by the atom type of the atoms bond to it.
The interaction styles listed below compute force field formulas that
are consistent with the OPLS-AA force field. See each command's
documentation for the formula it computes.
are fully or in part consistent with the OPLS style force fields. See
each command's documentation for the formula it computes. Some are only
compatible with a subset of OPLS interactions.
* :doc:`bond_style <bond_harmonic>` harmonic
* :doc:`angle_style <angle_harmonic>` harmonic
* :doc:`dihedral_style <dihedral_opls>` opls
* :doc:`improper_style <improper_cvff>` cvff
* :doc:`improper_style <improper_fourier>` fourier
* :doc:`improper_style <improper_harmonic>` harmonic
* :doc:`pair_style <pair_lj_cut_coul>` lj/cut/coul/cut
* :doc:`pair_style <pair_lj_cut_coul>` lj/cut/coul/long