Overview
This section covers the Alavi et al. 2005 (Alavi2005) force field as it is implemented into
the towhee_ff_Alavi2005 file in the ForceFields directory. All of the Towhee atom types for
this force field are listed, along with a short description of their meanings.
Note that this a Lennard-Jones (12-6) force field and can only be combined with
other Lennard-Jones (12-6) force fields.
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.
References for Alavi2005
This force field was published in a single paper where it was used along with the
SPC/E force field for water.
Alavi et al. 2005 in Towhee
The official force field name for Alavi et al. 2005 in Towhee is 'Alavi2005'.
This list contains all 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.
This force field was designed to work with the SPC/E water model.
This force field uses a three site model for H2 as described below.
Please note that the capitalization and spacing pattern is important and must be followed exactly as listed here.
- 'H2-com' : the center of mass of an H2 molecule. This atom type has no mass itself
and should be bonded to 2 H2-end sites.
- 'H2-end' : hydrogen atom in H2. This atom type represents the mass point for
each hydrogen atom and should be bonded to the H2-com site.
Coulombic interactions
Alavi2005 assigns a point charge to the H2 mass sites and also to the center of mass location.
The bond increment method is implemented for this forcefield and can be used to automatically assign
appropriate charges.
Here is a list of the bond increments using the bond names listed above. The value of the bond increment is added
to the first atom listed and subtracted from the second atom listed.
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