Overview
This section covers the Sum et al. 2003 United Atom (NERD) 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.
It is implemented in a separate file as the energy units in this paper are different from the previous ones and this results in minor
(and most likely insignificant) differences in the Carbon-Carbon bond energies.
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 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 Sum et al. 2003
The additional parameters for triglycerols designed to work with previosly published NERD force field parameters are published in a single paper.
Sum2003 in Towhee
The official force field name for Sum et al. 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 and made them consistent with the other NERD forcefield names.
Sum2003 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
- '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.
- '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.
- 'CHsp3oac' : sp3 carbon plus the 1 hydrogen bonded to it (united-atom) that is bonded
to an sp3 oxygen in a glycerol.
- 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
This 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.
Return to the Towhee Capabilities web page
|