Overview
This section covers the NERD Version 2 United Atom (NERD) force field as it is implemented into the towhee_ff_NERDv2 file in the ForceFields directory.
The NERD force field has had several minor changes to parameters as time as progresses so I have broken each of these changes into a different
version of the force field. All of the Towhee atom types for this force field are listed, along with a short description of their meanings.
Note that NERDv2 is a Lennard-Jones (12-6) force field and can only be combined with other Lennard-Jones (12-6) force fields.
I would like to thank Nicholas du Preez for initiating the implementation of this force field into Towhee.
Any discrepencies (especially typos) from the published values are the sole responsibility of Marcus Martin,
and I welcome feedback on how this implementation compares with other programs.
This forcefield was changed in version 8.1.0 so that the forcefield name is always just 'NERD' for all of the various implementations.
References for NERD Version 2
What I term NERD Version 2 is fully described in three papers. Please see the
NERDv1 documentation for more references to the original
work for this force field.
NERDv2 in Towhee
The official force field name for NERD Version 2 United Atom in Towhee is 'NERD'.
This list contains all of the atom names for use in the towhee_input file, along with a brief description.
I created these atom names in order to work with the molecule assembler.
NERDv2 is a united-atom force field that lumps hydrogens onto their neighboring carbons.
Note that hydrogens that are bonded to atoms other than carbon are not lumped onto their neighboring atoms.
The general pattern of the names is a list of the atoms that make up the group, followed by the hybridization of the central atom,
and ending in a character string that distinguishes similar atoms.
Please note that the capitalization and spacing pattern is important and must be followed exactly as listed here.
- sp3 hybridized Carbons
- 'CH4' : sp3 carbon plus the 4 hydrogens bonded to it (united-atom) in methane.
- 'CH3sp3eth' : sp3 carbon plus the 3 hydrogens bonded to it (united-atom) in ethane.
- 'CH3sp3pro' : sp3 carbon plus the 3 hydrogens bonded to it (united-atom) in propane.
- 'CH3sp3isob' : sp3 carbon plus the 3 hydrogens bonded to it (united-atom) in isobutane
(2-methylpropane).
- 'CH3sp32mb' : sp3 carbon plus the 3 hydrogens bonded to it (united-atom) bonded to
a CH group in 2-methylbutane.
- 'CH3sp3neop' : sp3 carbon plus the 3 hydrogens bonded to it (united-atom) bonded to
a C group in neopentane (2,2-dimethyl propane).
- 'CH3sp322db' : sp3 carbon plus the 3 hydrogens bonded to it (united-atom) bonded to
a C group in 2,2-dimethylbutane.
- 'CH3sp3pene' : sp3 carbon plus the 3 hydrogens bonded to it (united-atom) bonded to
an sp2 CH group in propene.
- 'CH3sp3mesc' : sp3 carbon plus the 3 hydrogens bonded to it (united-atom) bonded to
a CH group (methyl side-chain) and not a special case listed above.
- 'CH3sp3etsc' : sp3 carbon plus the 3 hydrogens bonded to it (united-atom) bonded to
a CH2 group that is itself bonded to a CH group (ethyl side-chain).
- 'CH3sp3gen' : sp3 carbon plus the 3 hydrogens bonded to it (united-atom) and not one
of the cases listed above.
- 'CH2sp3' : sp3 carbon plus the 2 hydrogens bonded to it (united-atom).
- 'CHsp3' : sp3 carbon plus the 1 hydrogen bonded to it (united-atom).
- 'Csp3' : sp3 carbon that is not bonded to any hydrogens.
- sp2 hybridized Carbons
- 'CH2sp2eth' : sp2 carbon plus the 2 hydrogens bonded to it (united-atom) in ethene.
- 'CH2sp2prim' : sp2 carbon plus the 2 hydrogens bonded to it (united-atom) in a primary alkene.
- 'CHsp2' : sp2 carbon plus the 1 hydrogen bonded to it (united-atom) in a primary alkene.
- Hydrogen
- 'H_s' : hydrogen bonded to sulfur.
- Sulfur
- 'S_sh2' : sulfur in dihydrogen sulfide.
Coulombic interactions
Most atoms do not have a charge when using the NERDv2 forcefield. Exceptions are listed below.
- 'H_s' : 0.124
- 'S_sh2' : -0.248
Improper torsions
This force field does not utilize improper torsions.
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