This section covers the NERD Version 1 United Atom (NERDv1) force field as it is implemented into
the towhee_ff_NERDv1 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. NERD Version 1 is mostly a subset of NERD Version 2, with the exception
that the linear alkane torsional potential is slightly different between the two versions.
All of the Towhee atom types for this force
field are listed, along with a short description of their meanings.
Note that NERDv1 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 G. Martin, and I welcome feedback on how this implementation compares
with other programs.
References for NERD Version 1
What I term NERD Version 1 is described in two papers.
NERDv1 in Towhee
The official force field name for NERD Version 1 United Atom in Towhee is 'NERDv1'. Here I list 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. NERDv1 is a united-atom force field which 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.
- '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.
- 'CH3sp32mb' : sp3 carbon plus the 3 hydrogens bonded to it (united-atom) bonded to
a CH group in 2-methylbutane.
- '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).
- 'CH2sp2eth' : sp2 carbon plus the 2 hydrogens bonded to it (united-atom) in ethene.
There are no coulombic interactions used in NERDv1, although there are some in subsequent versions of NERD.
This force field does not utilize improper torsions.
This force field does not have all of the groups needed for protein simulations.
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