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added Mie and Exp6 F mixing rules for non-LJ parameters in docs
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added Mie and Exp6 F mixing rules for non-LJ parameters in docs
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bc118 authored Jul 27, 2024
1 parent b1bbb68 commit ce84c04
Showing 1 changed file with 21 additions and 8 deletions.
29 changes: 21 additions & 8 deletions mosdef_dihedral_fit/dihedral_fit/fit_dihedral_with_gomc.py
Original file line number Diff line number Diff line change
Expand Up @@ -194,20 +194,33 @@ def fit_dihedral_with_gomc(
named 'dihedral.txt' for the energy and dihedral angle values (one 1 per directory).
combining_rule: str ('geometric' or 'lorentz'), default = None
The combining_rule in the foyer or GMSO XML file.
If this is None, it will use whatever is specified in the XML file, or the
default foyer or GMSO values. BEWARE, if it is not specified XML file, it has a default.
If this is None, it will use whatever is specified in the XML file,
or the default foyer or GMSO values.
The combining_rule in the foyer or GMSO XML file for the Lennard-Jones or VDW sigmas
(Rmin --> sigmas for Exp6). If this is None, it will use whatever is specified in
the XML file, or the default foyer or GMSO values. BEWARE, if it is not specified
XML file, it has a default. If this is None, it will use whatever is specified in
the XML file, or the default foyer or GMSO values.
'geometric' is the geometric mean used to combine the
Lennard-Jones or VDW sigmas, as required by OPLS force field.
Lennard-Jones or VDW sigmas (Rmin --> sigmas for Exp6), as required by OPLS force field.
'lorentz' is the arithmetic mean used to combine the
Lennard-Jones or VDW sigmas, as required by TraPPE, Amber, or CHARMM force fields.
Lennard-Jones or VDW sigmas (Rmin --> sigmas for Exp6), as required by
TraPPE, Amber, or CHARMM force fields.
'None', the default setting, is pulled from the force field XML, but if it is
'None', the default setting used to combine the Lennard-Jones or VDW sigmas
(Rmin --> sigmas for Exp6), is pulled from the force field XML, but if it is
not present it defaults to 'geometric' via MoSDeF's default settings.
NOTE: The mixing rules for the other non-Lennard-Jones or non-VDW sigmas forces are
listed below for reference, which applicable in GOMC and here:
"NOTE: epsilon_ij = 'geometric' for All FFs --> epsilon_ij = (epsilon_ii * epsilon_jj)**0.5."
"NOTE: n_ij = 'lorentz' for Mie FFs --> n_ij = (n_ii + n_jj)/2."
"NOTE: alpha_ij = 'geometric' for Exp FFs --> alpha_ij = (alpha_ii * alpha_jj)**0.5."
atom_type_naming_style: str, optional, default='all_unique', ('general' or 'all_unique')
* 'general'
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