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MCCCS Towhee (TraPPE United Atom)

 

 

Overview
    This section covers the TraPPE United Atom (TraPPE-UA) force field as it is implemented into the towhee_ff_TraPPE-UA file in the ForceFields directory. All of the Towhee atom types for the TraPPE United Atom force field are listed, along with a short description of their meanings. For more information about the TraPPE United Atom force field see the Siepmann group web site. Note that TraPPE United Atom 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 acknowledge Collin D. Wick, Jeff Potoff, and J. Ilja Siepmann for providing very useful guidance about implementing TraPPE-UA. Any discrepencies (especially typos) from the published TraPPE-UA force field values had better not exist considering I helped create this force field. The detail presented here for the TraPPE-UA force field is greater than the general level of detail for other forcefields due to the close relation between the authors of Towhee and TraPPE-UA. If someone does find a discrepancy with the published values I would be extremely grateful if they let me know about it. I welcome feedback on how this implementation compares with other programs.
References for TraPPE-UA Typos and comments for TraPPE-UA
    Here I list torsions that I believe are missing in the published TraPPE-UA papers. These torsions are therefore not implemented into Towhee.
      alkanes
    • CHx - CH - C - CHy torsion is missing. Example: 2,3,3-trimethylbutane.
    • CHx - C - C - CHy torsion is missing. Example: 2,2,3,3-quatramethylbutane.
    • alkenes
    • CHx - CH2(sp3) - C(sp2 double bonded to C) - CHy torsion is missing. Example: 2-methyl-1-butene torsion involving only single bonds.
    • CHx - CH(sp3) - C(sp2 double bonded to C) - CHy torsion is missing. Example: 2,3-dimethyl-1-butene torsion involving only single bonds.
    • CHx - C(sp3) - C(sp2 double bonded to C) - CHy torsion is missing. Example: 2,3,3-trimethyl-1-butene torsion involving only single bonds.
    • alcohols
    • CHx - CH2 - CH - OH torsion is missing. Example: 1-methylethanol.
    • CHx - CH2 - C - OH torsion is missing. Example: 1,1-dimethylethanol.
    • CHx - CH2 - C - OH torsion is missing. Example: 1,1,1-trimethylethanol.
    • ketones
    • CHx - CH2(sp3) - C(sp2 double bonded to O) - CHy torsion is missing. Example: buta-2-one torsion involving only single bonds.
    • CHx - CH(sp3) - C(sp2 double bonded to O) - CHy torsion is missing. Example: 3-methylbuta-2-one torsion involving only single bonds.
    • CHx - C(sp3) - C(sp2 double bonded to O) - CHy torsion is missing. Example: 3,3-dimethylbuta-2-one torsion involving only single bonds.
    • ethers
    • CHx - CH2(sp3) - CH(sp3) - O torsion is missing. Example: sec-butyl ethyl ether.
    • CHx - CH(sp3) - CH(sp3) - O torsion is missing. Example: 1,2-dimethylpropyl ethyl ether.
    • CHx - C(sp3) - CH(sp3) - O torsion is missing. Example: 1,2,2-trimethylpropyl ethyl ether.
    • CHx - CH2(sp3) - C(sp3) - O torsion is missing. Example: 1,1-dimethylpropyl ethyl ether.
    • CHx - CH(sp3) - C(sp3) - O torsion is missing. Example: 1,1,2-trimethylpropyl ethyl ether.
    • CHx - C(sp3) - C(sp3) - O torsion is missing. Example: 1,1,2,2-quatramethylpropyl ethyl ether.

    A few angles for carboxylic acids were not listed in the Kamath et al. 2004 paper and here I list the missing angle terms and then also list the terms Jeff Potoff suggested for use with these angles.
    • CH2 - C(acid) - O in carboxylic acid is not listed. I used the similar CH3 - C(acid) - O parameters.
    • CH2 - C(acid) = O in carboxylic acid is not listed. I used the similar CH3 - C(acid) = O parameters.
    The functional form for one of the torsions was listed incorrectly in Equation 5 of the Kamath et al. 2004 paper. That paper lists the torsion as
      Utorsion = c1[ 1 + cos( &phi + f1 )] + c2 [ 1 - cos(2 &phi)]
    but the actual torsion potential used in that work (according to personal communication with Jeff Potoff) is
      Utorsion = c1[ 1 + cos( &phi + f1 )] + c2 [ 1 - cos2(&phi)]
    and this correction was made in Towhee beginning with version 4.6.1.
    A few torsions for carboxylic acids were not listed in the Kamath et al. 2004 paper and here I list the missing torsion terms and then also list the terms Jeff Pottof suggested for use with these torsions.
    • CHx - CH2 - C(acid) = O in carboxylic acid is not listed. This uses the OCOH carboxylic torsion.
    • CHx - CH2 - C(acid) - O in carboxylic acid is not listed. This uses the linear alkane CHx - CH2 - CH2 - CHx torsion.
    The functional form used for alkenes is listed incorrectly in Equation 5 of the Wick et al. 2000 paper. That equation should read
      utors = d0 (&phi - &phi0)2
TraPPE-UA in Towhee
    The official force field name for TraPPE United Atom in Towhee is 'TraPPE-UA'. Here I list all of the TraPPE-UA 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. TraPPE-UA 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 naming convention listed here began with version 4.4.1 as some changed were required in order to implement TraPPE-6. The general pattern of the names is a list of the atoms that make up the group, followed by the types of atoms that they are single bonded to, followed by the atoms they are double bonded to (prefixed with an '='), and ending in a code that represents the bonding pattern of the atom. The Bond Name is also listed to facilitate comparision with the bond increment method listed down in the coulombic section. Please note that the capitalization and spacing pattern is important and must be followed exactly as listed here.
      Argon
    • 'Ar' : argon
    • Carbon (not bonded to any hydrogens)
    • 'Ccccc(sp3)' : an sp3 carbon. This atom is single bonded to four carbon atoms. Bond name Csp3.
    • 'Cccco(sp3)' : an sp3 carbon. This atom is single bonded to three carbon atoms and single bonded to one oxygen atom. Bond name Csp3.
    • 'Ccc=c(sp2)' : an sp2 carbon. This atom is single bonded to two carbon atoms and double bonded to one carbon atom. Bond name Csp2.
    • 'Ccc=o(sp2)' : an sp2 carbon. This atom is single bonded to two carbon atoms and double bonded to one oxygen atom. Bond name Ccc=o(sp2).
    • 'Cco=o(sp2)' : an sp2 carbon. This atom is single bonded to one carbon atom, single bonded to one oxygen atom, and double bonded to one oxygen atom. Bond name Cco=o(sp2).
    • 'Caac(aro)' : an aromatic carbon. This atom is bonded to two aromatic carbon atoms and single bonded to one carbon atom. Bond name Caro.
    • 'Caaa(aro)' : an aromatic carbon. This atom is bonded to three aromatic carbon atoms. Bond name Caro.
    • Carbon (united atom including 1 bonded hydrogen)
    • 'CHccc(sp3)' : united-atom consisting of an sp3 carbon and one bonded hydrogen. This united-atom is single bonded to three carbon atoms. Bond name Csp3.
    • 'CHcco(sp3)' : united-atom consisting of an sp3 carbon and one bonded hydrogen. This united-atom is single bonded to two carbon atoms and single bonded to one oxygen atom. Bond name Csp3.
    • 'CHc=c(sp2)' : united-atom consisting of an sp2 carbon and one bonded hydrogen. This united-atom is single bonded to one carbon atom and double bonded to one carbon atom. Bond name Csp2.
    • 'CHc=o(sp2)' : united-atom consisting of an sp2 carbon and one bonded hydrogen. This united-atom is single bonded to one carbon atom and double bonded to one oxygen atom. Bond name CHc=o(sp2).
    • 'CHaa(aro)' : united-atom consisting of an aromatic carbon and one bonded hydrogen. This united-atom is bonded to two aromatic carbon atoms. Bond name Caro.
    • Carbon (united atom including 2 bonded hydrogens)
    • 'CH2**(sp3)' : united-atom consisting of an sp3 carbon and two bonded hydrogens. This united-atom is single bonded to any two non-hydrogen atoms. Bond name Csp3.
    • 'CH2=*(sp2)' : united-atom consisting of an sp2 carbon and two bonded hydrogens. This united-atom is double bonded to any one non-hydrogen atom. Bond name Csp2.
    • Carbon (united atom including 3 bonded hydrogens)
    • 'CH3*(sp3)' : united-atom consisting of an sp3 carbon and three bonded hydrogens. This united-atom is single bonded to any non-hydrogen atom. Bond name Csp3.
    • Carbon (united atom including 4 bonded hydrogens)
    • 'CH4' : methane
    • Helium
    • 'He' : helium
    • Hydrogen (not bonded to a carbon)
    • 'Ho' : hydrogen bonded to one oxygen. Bond name Ho.
    • 'Hoacid' : hydrogen bonded to one oxygen in a carboxylic acid. Bond name Hoacid.
    • Oxygen
    • 'Och(sp3)' : sp3 oxygen atom that is single bonded to one carbon atom and single bonded to one hydrogen atom. Bond name Och(sp3).
    • 'Occ(sp3)' : sp3 oxygen atom that is single bonded to two carbon atoms. Bond name Occ(sp3).
    • 'O=c(sp2)' : sp2 oxygen atom that is double bonded to one carbon atom. Bond name O=c(sp2).
TraPPE-UA and the Molecule Assembler
    The molecule builder is only partially functional for TraPPE-UA. The builder can assemble aliphatic hydrocarbons and alcohols, but it does not work for aromatics. In the case of alkenes, TraPPE-UA has different torsional potentials for cis and trans and these can be distinguished using the options in the 'advanced connectivity map'. TraPPE-UA also uses a rigid model for aromatics, which is currently problematic for Towhee.
Coulombic interactions
    TraPPE-UA uses atom-centered point charges to represent the electrostatic interactions. Generally, there is no charge on any of the hydrocarbons, but there are exceptions once other atoms are mixed into the molecules. Note that there is a 0.5 scaled 1-4 coulombic interaction built into the most of the torsional potentials. This general rule is contradicted by some of the torsions for carboxylic acids. You can take a look at the TraPPE-UA force field literature to determine how to assign the charges, or you can try out the 'bond increment' method for assigning charges on these molecules. Here I list 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.
    • Csp3 - Csp3: 0.0
    • Csp3 - Csp2: 0.0
    • Csp3 - Caro: 0.0
    • Csp2 - Csp2: 0.0
    • Caro - Caro: 0.0
    • Ho - Och(sp3): 0.435
    • Csp3 - Och(sp3): 0.265
    • Csp3 - Occ(sp3): 0.25
    • CHc=o(sp2) - Csp3: 0.043
    • CHc=o(sp2) - O=c(sp2): 0.482
    • Ccc=o(sp2) - O=c(sp2): 0.424
    • O=c(sp2) - Cco=o(sp2): -0.45
    • Csp3 - Cco=o(sp2): 0.12
    • Och(sp3) - Cco=o(sp2): -0.09
    • Hoacid - Och(sp3): 0.37
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Send comments to: Marcus G. Martin

Last updated: January 09, 2007