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minor math formatting changes after phone readability testing, and added note box to use tip3 with charmm

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alphataubio
2024-01-06 19:49:43 -05:00
parent 9a97906fe5
commit 2643a94f79
1 changed files with 8 additions and 4 deletions
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doc/src/Howto_bioFF.rst
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@ -20,18 +20,18 @@ The `CHARMM force field <https://mackerell.umaryland.edu/charmm_ff.shtml>`_ :ref
.. math:: .. math::
V = & \sum_{bonds} E_b + \sum_{angles} \!E_a + \!\overbrace{\sum_{dihedral} \!\!E_d}^{\substack{ V & = \sum_{bonds} E_b + \sum_{angles} \!E_a + \!\overbrace{\sum_{dihedral} \!\!E_d}^{\substack{
\text{charmm} \\ \text{charmm} \\
\text{charmmfsw} \text{charmmfsw}
}} +\!\! \sum_{impropers} \!\!\!E_i + \!\!\!\!\!\!\overbrace{\sum_{pairs} \left(E_{LJ}+E_{coul}\right)}^{\substack{ }} +\!\!\! \sum_{impropers} \!\!\!E_i \\[.6em]
& \quad + \!\!\!\!\!\!\!\!\!\!\underbrace{~\sum_{pairs} \left(E_{LJ}+E_{coul}\right)}_{\substack{
\text{lj/charmm/coul/charmm} \\ \text{lj/charmm/coul/charmm} \\
\text{lj/charmm/coul/charmm/implicit} \\ \text{lj/charmm/coul/charmm/implicit} \\
\text{lj/charmm/coul/long} \\ \text{lj/charmm/coul/long} \\
\text{lj/charmm/coul/msm} \\ \text{lj/charmm/coul/msm} \\
\text{lj/charmmfsw/coul/charmmfsh} \\ \text{lj/charmmfsw/coul/charmmfsh} \\
\text{lj/charmmfsw/coul/long} \text{lj/charmmfsw/coul/long}
}} \\[0.6em] }} \!\!\!\!\!\!\!\!+ \!\!\sum_{special}\! E_s + \!\!\!\!\sum_{residues} \!\!\!{\scriptstyle\mathrm{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. 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.
@ -112,6 +112,10 @@ These styles are used by LAMMPS input scripts generated by `charmm-gui.org <http
<pair_charmm>` and :doc:`dihedral charmm <dihedral_charmm>` doc <pair_charmm>` and :doc:`dihedral charmm <dihedral_charmm>` doc
pages. pages.
.. note::
TIP3P water model MUST be used with CHARMM force field not TIP4P, TIP5P or SPC. In fact, `"using the SPC model with CHARMM parameters is a bad idea" <https://matsci.org/t/using-spc-water-with-charmm-ff/24715>`_ and `"to enable TIP4P style water in CHARMM, you would have to write a new pair style" <https://matsci.org/t/hybrid-pair-styles-for-charmm-and-tip4p-ew/32609>`_ . LAMMPS input scripts generated by Solution Builder on charmm-gui.org use TIP3P molecules for solvation. Any other water model can and probably will lead to false conclusions.
COMPASS COMPASS
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