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MCCCS Towhee (NERD Version 3)

 

 

Overview
    This section covers the NERD Version 3 United Atom (NERDv3) force field as it is implemented into the towhee_ff_NERDv3 file in the ForceFields directory. The NERD force field has had several minor changes to parameters as time as progresses so I have broken each of these changes into a different version of the force field. All of the Towhee atom types for this force field are listed, along with a short description of their meanings. Note that NERDv3 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 thank Nicholas du Preez for initiating the implementation of this force field into Towhee. 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 NERD Version 3
    What I term NERD Version 3 is described in a single paper (listed here) plus all of the original NERDv1 and NERDv2 references. Note that some of the terms in those original works have been superceded by later publications.
NERDv3 in Towhee
    The official force field name for NERD Version 2 United Atom in Towhee is 'NERDv3'. 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. NERDv3 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
    • 'CH4' : sp3 carbon plus the 4 hydrogens bonded to it (united-atom) in methane.
    • 'CH3sp3eth' : sp3 carbon plus the 3 hydrogens bonded to it (united-atom) in ethane.
    • 'CH3sp3pro' : sp3 carbon plus the 3 hydrogens bonded to it (united-atom) in propane.
    • 'CH3sp3isob' : sp3 carbon plus the 3 hydrogens bonded to it (united-atom) in isobutane (2-methylpropane).
    • 'CH3sp32mb' : sp3 carbon plus the 3 hydrogens bonded to it (united-atom) bonded to a CH group in 2-methylbutane.
    • 'CH3sp3neop' : sp3 carbon plus the 3 hydrogens bonded to it (united-atom) bonded to a C group in neopentane (2,2-dimethyl propane).
    • 'CH3sp322db' : sp3 carbon plus the 3 hydrogens bonded to it (united-atom) bonded to a C group in 2,2-dimethylbutane.
    • 'CH3sp3pene' : sp3 carbon plus the 3 hydrogens bonded to it (united-atom) bonded to an sp2 CH group in propene.
    • '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.
    • 'CH2sp3' : sp3 carbon plus the 2 hydrogens bonded to it (united-atom).
    • 'CHsp3' : sp3 carbon plus the 1 hydrogen bonded to it (united-atom).
    • 'Csp3' : sp3 carbon that is not bonded to any hydrogens.
    • sp2 hybridized Carbons
    • 'CH2sp2eth' : sp2 carbon plus the 2 hydrogens bonded to it (united-atom) in ethene.
    • 'CH2sp2prim' : sp2 carbon plus the 2 hydrogens bonded to it (united-atom) in a primary alkene.
    • 'CHsp2' : sp2 carbon plus the 1 hydrogen bonded to it (united-atom) in a primary alkene.
    • Hydrogen
    • 'H_o' : hydrogen bonded to oxygen.
    • 'H_s' : hydrogen bonded to sulfur.
    • Oxygen
    • 'Osp3' : sp3 hybridized oxygen single bonded to two atoms.
    • Sulfur
    • 'S_sh2' : sulfur in dihydrogen sulfide.
Coulombic interactions
    Most atoms do not have a charge when using the NERDv3 forcefield. Exceptions are listed below.
    SH2 (from Nath 2003)
  • 'H_s' : 0.124
  • 'S_sh2' : -0.248
  • alcohols (from Khare et al. 2004)
  • 'H_o' : 0.420
  • 'Osp3' : -0.710
  • 'CH2sp3' (bonded to the oxygen): 0.290
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