diff --git a/doc/src/Howto_bioFF.rst b/doc/src/Howto_bioFF.rst index c5cd8f1f0b..35aa609e5a 100644 --- a/doc/src/Howto_bioFF.rst +++ b/doc/src/Howto_bioFF.rst @@ -20,18 +20,18 @@ The `CHARMM force field `_ :ref .. 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{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/implicit} \\ \text{lj/charmm/coul/long} \\ \text{lj/charmm/coul/msm} \\ \text{lj/charmmfsw/coul/charmmfsh} \\ \text{lj/charmmfsw/coul/long} - }} \\[0.6em] - & \qquad \!\!\!\!+ \sum_{special}\! E_s + \sum_{residues} \!\text{CMAP}(\phi,\psi) + }} \!\!\!\!\!\!\!\!+ \!\!\sum_{special}\! E_s + \!\!\!\!\sum_{residues} \!\!\!{\scriptstyle\mathrm{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 ` 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) `. 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 ` and :doc:`dihedral charmm ` doc 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" `_ and `"to enable TIP4P style water in CHARMM, you would have to write a new pair style" `_ . 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 -------