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MCCCS Towhee (Sum et al. 2003)

 

 

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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Send comments to: Marcus G. Martin
Last updated: September 07, 2005