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fixed latex missing $ error and added little bit of negative spaces

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alphataubio
2024-01-06 17:22:28 -05:00
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doc/src/Howto_bioFF.rst
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@ -23,15 +23,15 @@ The `CHARMM force field <https://mackerell.umaryland.edu/charmm_ff.shtml>`_ :ref
V = & \sum_{bonds} E_b + \sum_{angles} \!E_a + \!\overbrace{\sum_{dihedral} \!\!E_d}^{\substack{
\text{charmm} \\
\text{charmmfsw}
}} +\!\! \sum_{impropers} \!\!\!E_i + \!\!\!\!\overbrace{\sum_{pairs} \left(E_{LJ}+E_{coul}\right)}^{\substack{
}} +\!\! \sum_{impropers} \!\!\!E_i + \!\!\!\!\!\!\overbrace{\sum_{pairs} \left(E_{LJ}+E_{coul}\right)}^{\substack{
\text{lj/charmm/coul/charmm} \\
\text{lj/charmm/coul/charmm/implicit} \\
\text{lj/charmm/coul/long} \\
\text{lj/charmm/coul/msm} \\
\text{lj/charmmfsw/coul/charmmfsh} \\
\text{lj_charmmfsw/coul/long}
\text{lj/charmmfsw/coul/long}
}} \\[0.6em]
& \qquad \!\!\!\!+ \sum_{special}\! E_s + \sum_{residues} \text{CMAP}(\phi,\psi)
& \qquad \!\!\!\!+ \sum_{special}\! E_s + \sum_{residues} \!\text{CMAP}(\phi,\psi)
The terms are computed by bond styles (relationship between 2 atoms), angle styles (between 3 atoms) , dihedral/improper styles (between 4 atoms), pair styles (non-covalently bonded pair interactions) and special bonds. The CMAP term (see :doc:`fix cmap <fix_cmap>` command for details) corrects for pairs of dihedral angles ("Correction MAP") to significantly improve the structural and dynamic properties of proteins in crystalline and solution environments :ref:`(Brooks) <howto-Brooks>`. The AMBER force field does not include the CMAP term.