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Overview
This section covers the Sum et al. 2003 United Atom (Sum2003) force field as it is implemented into
the towhee_ff_Sum2003 file in the ForceFields directory. This forcefield is an extension to the
NERDv2 force field that allows the simulation of acetates and glycerols.
I would like to acknowledge Mary Biddy for providing useful guidence about implementing this force field.
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 Sum et al. 2003
See the NERD Version 2 force field documentation for the references for the
alkane chains. The extensions to that force field are published in a single paper.
Sum2003 in Towhee
The official force field name for Sum et al. United Atom in Towhee is 'Sum2003'. 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. Sum2003 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.
- sp3 hybridized Carbons
- 'CH3sp3oac' : sp3 carbon plus the 3 hydrogens bonded to it (united-atom) bonded to
an sp3 oxygen in an acetate group.
- 'CH3sp3cac' : sp3 carbon plus the 3 hydrogens bonded to it (united-atom) bonded to
an sp2 carbon in an acetate group.
- '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.
- 'CH2sp3oac' : sp3 carbon plus the 2 hydrogens bonded to it (united-atom) that is bonded
to an sp3 oxygen in a glycerol.
- 'CH2sp3cac' : sp3 carbon plus the 2 hydrogens bonded to it (united-atom) that is bonded
to an sp2 carbon in an acetate group.
- 'CH2sp3' : sp3 carbon plus the 2 hydrogens bonded to it (united-atom) and not a special case.
- 'CHsp3oac' : sp3 carbon plus the 1 hydrogen bonded to it (united-atom) that is bonded
to an sp3 oxygen in a glycerol.
- 'CHsp3' : sp3 carbon plus the 1 hydrogen bonded to it (united-atom) and not a special case.
- 'Csp3' : sp3 carbon that is not bonded to any hydrogens.
- sp2 hybridized Carbons
- 'Csp2ac' : sp2 carbon double bonded to an sp2 oxygen, single bonded to
an sp3 oxygen, and single bonded to another carbon in an acetate group.
- Oxygen
- 'Osp3' : sp3 oxygen bonded to two atoms.
- 'Osp2' : sp2 oxygen double bonded to a single atom.
Coulombic interactions
Here is the list of charge assignments for methylacetate. It appears that these are also the charges used
for an acetate headgroup on other molecules (e.g. glycerols).
- 'CH3sp3oac' : 0.200
- 'Osp3' : -0.400
- 'Csp2ac' : 0.650
- 'Osp2' : -0.500
- 'CH3sp3cac' : 0.050
Improper torsions
This force field does not utilize improper torsions.
Proteins
This force field does not have all of the groups needed for protein simulations.
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