This section covers the Dubbeldam et al. (Dubb2004) force field as it is implemented into
the towhee_ff_Dubb2004 file in the ForceFields directory. This force field is for adsorption
simulations of alkanes in various Zeolites.
Note that this is a Lennard-Jones force field that uses explicit mixing rules so it is not
easily combined with other force fields.
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 Dubb2004
What I term Dubb2004 is described in several papers.
In addition, some of their torsional interactions are overly complicated. The torsions
involving the CH group are specified in terms of where the hydrogen would be if it was explicitly
included in the simulation. Thijs Vlugt suggested replacing the torsions involving the CH group
with those from the TraPPE-UA forcefield and I have followed that suggestion for this implementation.
Dubb2004 in Towhee
The official force field name for Dubbeldam et al. United Atom in Towhee is 'Dubb2004'. 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. Dubb2004 is a united-atom force field which lumps
hydrogens onto their neighboring carbons. It is also designed for work with Silaceous and aluminum substituted
zeolites. 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.
- 'CH3' : sp3 carbon plus the 3 hydrogens bonded to it (united-atom) in ethane.
- 'CH2' : sp3 carbon plus the 2 hydrogens bonded to it (united-atom).
- 'CH' : sp3 carbon plus the 1 hydrogen bonded to it (united-atom).
- 'C' : sp3 carbon that is not bonded to any hydrogens.
- Zeolite Framework Atoms
- 'O' : oxygen bonded to silicon and/or aluminum in the zeolite framework.
- 'Si' : silicon bonded to four oxygens in the zeolite framework.
- 'Al' : aluminum bonded to four oxygens in the zeolite framework.
- Zeolite Counter Ions
- 'Na' : sodium ion.
There are specific charge assignents for the atoms in the zeolite framework and these assignments are enforced
by the angle potential for the zeolite. There are no charges on the alkane united-atoms. The 'bond increment'
method of charge_assignment is implemented for this forcefield.
Please see the inpstyle 2 documentation for
further information on enabling this option. Otherwise, you are welcome to manually set the charges. Here I
list the charges that are assigned by the 'bond increment' method.
Return to the Towhee Capabilities web page
- 'Si' : 2.05
- 'Al' : 1.75
- 'O' bonded to two silicons: -1.025
- 'O' bonded to one silicon and one aluminum: -1.20
- 'Na' : 1.0
- 'C' : all alkane carbons have a 0.0 charge.