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MCCCS Towhee (towhee_input classical_potential)

 

 

classical_potential (character*30)
    The different settings for classical_potential require a different set of variables afterwards. For each classical_potential a description of the nonbonded potential and the set of subsequent required variables is listed. This documentation is only kept up to date for the most current release version. Last updated for version 7.0.5.
  • '12-6 plus 12-10 H-bond': 12-6 Lennard-Jones plus a 12-10 hydrogen bonding term on certain pairs
      This uses the standard Lennard-Jones 12-6 plus an extra 12-10 term between certain pairs of atoms that are identified as hydrogen bond donors and accepters. See Weiner et al. 1984 for more information.
      If the two atoms are separated by more than 3 bonds, or are on different molecules then
      Unonbond = 4 * nbcoeff(2) * [ (nbcoeff(1)/r)12 - (nbcoeff(1)/r)6 ] + hbondcoeff(1) / r12 - hbondcoeff(2) / r10
      else if the two atoms are separated by exactly 3 bonds then
      Unonbond = 4 * nbcoeff(4) * [ (nbcoeff(3)/r)12 - (nbcoeff(3)/r)6 ] + hbondcoeff(1) / r12 - hbondcoeff(2) / r10
      classical_mixrule (character*30)
        This variable specifies the manner in which the parameters for unlike atoms are determined.
      • 'Lorentz-Berthelot': arithmetic mean of σ values [nbcoeff(1) or nbcoeff(3)], geometric mean of ε values [nbcoeff(2) or nbcoeff(4)].
      • 'Shukla': complicated expression involving the polarizability of each atom. See equations 19 and 20 of Shukla 1987 for the definition of this mixing rule.
      lshift See the lshift section for information about this variable
      ltailc See the ltailc section for information about this variable
      rmin See the rmin section for information about this variable
      rcut See the rcut section for information about this variable
      rcutin See the rcutin section for information about this variable
  • '12-6 plus solvation': 12-6 Lennard-Jones with implicit solvent
      This uses the standard Lennard-Jones 12-6 plus an extra implicit solvation term. See Lazaridis and Karplus 1999 for more information.
      If the two atoms are separated by more than 3 bonds, or are on different molecules then
      Unonbond = 4 * nbcoeff(2) * [ (nbcoeff(1)/r)12 - (nbcoeff(1)/r)6 ]
      else if the two atoms are separated by exactly 3 bonds then
      Unonbond = 4 * nbcoeff(4) * [ (nbcoeff(3)/r)12 - (nbcoeff(3)/r)6 ]
      classical_mixrule (character*30)
        This variable specifies the manner in which the parameters for unlike atoms are determined.
      • 'Geometric': geometric mean of all nonbonded coefficients.
      • 'Explicit': cross terms explicitly defined in the appropriate towhee_ff file.
      lshift See the lshift section for information about this variable
      ltailc See the ltailc section for information about this variable
      rmin See the rmin section for information about this variable
      rcut See the rcut section for information about this variable
      rcutin See the rcutin section for information about this variable

  • '12-9-6': 12-9-6 potential
      This variant of the Lennard-Jones family of potentials was implemented for force fields that use a combination of 12-6 and 9-6.
      v(r) = nbcoeff(1) * (1/r)12 + nbcoeff(2) * (1/r)9 + nbcoeff(3) * (1/r)6
      classical_mixrule (character*30)
        This variable specifies the manner in which the parameters for unlike atoms are determined.
      • 'Geometric': geometric mean of the nonbonded coefficients.
      • 'Explicit': cross terms explicitly defined in the appropriate towhee_ff file.
      lshift See the lshift section for information about this variable
      ltailc See the ltailc section for information about this variable
      rmin See the rmin section for information about this variable
      rcut See the rcut section for information about this variable
      rcutin See the rcutin section for information about this variable

  • '9-6': 9-6 potential
      If the two atoms are separated 3 or more bonds, or are on different molecules then
      Unonbond = nbcoeff(2) * [ 2*(nbcoeff(1)/r)9 - 3*(nbcoeff(1)/r)6 ]
      classical_mixrule (character*30)
        This variable specifies the manner in which the parameters for unlike atoms are determined.
      • 'Sixth Power': sixth order combination of σ and ε of Waldman and Hagler 1993.
      lshift See the lshift section for information about this variable
      ltailc See the ltailc section for information about this variable
      rmin See the rmin section for information about this variable
      rcut See the rcut section for information about this variable
      rcutin See the rcutin section for information about this variable

  • 'Buffered 14-7': Buffered 14-7 potential
      If the two atoms are separated 3 or more bonds, or are on different molecules then
      Unonbond(r) = εIJ [ (1.07 RIJ) / (r + 0.07 RIJ) ] * [ (1.12 RIJ7 ) / (r7 + 0.12 RIJ7) ]
      where the εIJ and RIJ parameters are determined for each pair of interactions (I and J) using the mixing rules. The nonbonded coefficients required for this forcefield are as follows.
      • nbcoeff(1): alpha-i in the MMFF94 native units
      • nbcoeff(2): N-i in the MMFF94 native units
      • nbcoeff(3): A-i in the MMFF94 native units
      • nbcoeff(4): G-i in the MMFF94 native units
      classical_mixrule (character*30)
        This variable specifies the manner in which the parameters for unlike atoms are determined.
      • 'MMFF': the mixing rules used to determine εIJ and RIJ from the four nonbonded coefficients as described in the second MMFF94 paper (Halgren 1996 (II)).
      ltailc See the ltailc section for information about this variable. This option is not yet implemented properly as it is surprisingly difficult to integrate the Buffered 14-7 form, but hopefully it will be functioning soon.
      rmin See the rmin section for information about this variable
      rcut See the rcut section for information about this variable
      rcutin See the rcutin section for information about this variable

  • 'Double Exponential': Double exponential potential
      If the two atoms are separated by 3 or more bonds, or are on different molecules then
      Unonbond = nbcoeff(1) * Exp[ - nbcoeff(2) r] - nbcoeff(3) * Exp[ - nbcoeff(4) r]
      classical_mixrule (character*30)
        This variable specifies the manner in which the parameters for unlike atoms are determined.
      • 'Explicit': cross terms explicitly specified in the appropriate towhee_ff file.
      lshift See the lshift section for information about this variable
      ltailc See the ltailc section for information about this variable
      rmin See the rmin section for information about this variable
      rcut See the rcut section for information about this variable
      rcutin See the rcutin section for information about this variable

  • 'Embedded Atom Method': Embedded Atom Method (see Daw and Baskes 1983)
      This is an atomic potential and can only be used with monatomic molecules in Towhee. Historically, the Embedded Atom Method (EAM) uses a lookup table for computing intermolecular interactions and this is an option in Towhee. When tabular data is used the interpolatestyle determines the method for interpolating between the specified values. Other functional forms are allowed as described in the Towhee Force Field Documentation. EAM is a short-ranged potential that captures many-body effects by computing a local density about each atom. This so-called local density is actually a distance dependent function. The sum of the local densities is then fed into the embedding function to compute the embedding energy. Additionally, there is a pair potential term.
      interpolatestyle See the interpolatestyle section for information about this variable
      rcut See the rcut section for information about this variable

  • 'EAM pair only': Embedded Atom Method (see Daw and Baskes 1983) using only the pair potential
      This is is the same as the Embedded Atom Method, but only utilizes the pair potential portion and omits the embedding energy. This option exists for academic study of the pair potential portion of the Embedded Atom Method functions. It reads from the same potential files as the 'Embedded Atom Method' potential.
      interpolatestyle See the interpolatestyle section for information about this variable
      rcut See the rcut section for information about this variable

  • 'Exponential-12-6': Exponential plus 12-6 Lennard-Jones potential
      If the two atoms are separated by more than 3 bonds, or are on different molecules then
      Unonbond = nbcoeff(1)/r^6 + nbcoeff(2)/r^12 + nbcoeff(3)*exp[nbcoeff(4)*r]
      classical_mixrule (character*30)
        This variable specifies the manner in which the parameters for unlike atoms are determined.
      • 'Explicit': cross terms explicitly defined in the appropriate towhee_ff file.
      lshift See the lshift section for information about this variable
      ltailc See the ltailc section for information about this variable
      rmin See the rmin section for information about this variable
      rcut See the rcut section for information about this variable
      rcutin See the rcutin section for information about this variable

  • 'Exponential-6': Exponential-6 potential
      If the two atoms are separated by more than 3 bonds, or are on different molecules then
      Unonbond = nbcoeff(1)/r^6 + nbcoeff(2) * exp[nbcoeff(3)*r]
      classical_mixrule (character*30)
        This variable specifies the manner in which the parameters for unlike atoms are determined.
      • 'Explicit': cross terms explicitly defined in the appropriate towhee_ff file.
      lshift See the lshift section for information about this variable
      ltailc See the ltailc section for information about this variable
      rcut See the rcut section for information about this variable
      rcutin See the rcutin section for information about this variable

  • 'Gordon n-6': shifted n-6 potential of Peter Gordon.
      Designed to have the position and depth of the minimum in the potential well to correspond with that of a 12-6 Lennard-Jones potential.
      Unonbond = 4 * nbcoeff(2) * c(n) * [ {nbcoeff(1)/(r-a(n))}n - {nbcoeff(1)/(r-a(n))}6 ]
      a(n) = [ 21/6 - (n/6)1/(n-6) ] * nbcoeff(1)
      rminimum = a(n) + (n/6)1/(n-6) * nbcoeff(1)
      c(n) = -(1/4)*[ 1 / ( (nbcoeff(1)/(rminimum - a(n)))n - ( nbcoeff(1) / (rminimum - a(n)) )6 )]
      classical_mixrule (character*30)
        This variable specifies the manner in which the parameters for unlike atoms are determined.
      • 'Lorentz-Berthelot': arithmetic mean of σ[nbcoeff(1)], geometric mean of ε[nbcoeff(2)]
      lshift See the lshift section for information about this variable
      ltailc See the ltailc section for information about this variable
      rmin See the rmin section for information about this variable
      rcut See the rcut section for information about this variable
      rcutin See the rcutin section for information about this variable

  • 'Hard 2580 Multistep': Hard core multistep potential
      If the two atoms are separated by more than 3 bonds, or are on different molecules, then
      If r < nbcoeff(1)
        Unonbond = Infinity
      else if nbcoeff(1) <= r < 1.2 * nbcoeff(1)
        Unonbond = nbcoeff(2)
      else if 1.2 * nbcoeff(1) <= r < 1.5 * nbcoeff(1)
        Unonbond = nbcoeff(3)
      else if 1.5 * nbcoeff(1) <= r < 1.8 * nbcoeff(1)
        Unonbond = nbcoeff(4)
      else if 1.8 * nbcoeff(1) <= r < 2.0 * nbcoeff(1)
        Unonbond = nbcoeff(5)
      else if 2.0 * nbcoeff(1) <= r
        Unonbond = 0.0
      classical_mixrule (character*30)
        This variable specifies the manner in which the parameters for unlike atoms are determined.
      • 'Lorentz-Berthelot': arithmetic mean of σ values, geometric mean of well depths.
      radial_pressure_delta See the radial_pressure_delta section for information about this variable

  • 'Hard Sphere': Hard Sphere potential
      If the two atoms are separated by more than 3 bonds, or are on different molecules, then
      Unonbond = Infinity if r <= nbcoeff(1), or 0 otherwise
      classical_mixrule (character*30)
        This variable specifies the manner in which the parameters for unlike atoms are determined.
      • 'Arithmetic': arithmetic mean of σ.
      radial_pressure_delta See the radial_pressure_delta section for information about this variable

  • 'Lennard-Jones': 12-6 Lennard-Jones potential.
      If the two atoms are separated by more than 3 bonds, or are on different molecules then
      Unonbond = 4 * nbcoeff(2) * [ (nbcoeff(1)/r)12 - (nbcoeff(1)/r)6 ]
      else if the two atoms are separated by exactly 3 bonds then
      Unonbond = 4 * nbcoeff(4) * [ (nbcoeff(3)/r)12 - (nbcoeff(3)/r)6 ]
      classical_mixrule (character*30)
        This variable specifies the manner in which the parameters for unlike atoms are determined.
      • 'Lorentz-Berthelot': arithmetic mean of σ, geometric mean of ε
      • 'Geometric': geometric mean of σ and ε
      • 'Explicit': cross terms explicitly specified in the appropriate towhee_ff file.
      • 'Shukla': complicated expression involving the polarizability of each atom. See equations 19 and 20 of Shukla 1987 for the definition of this mixing rule.
      • 'LB plus manual': uses the Lorentz-Berthelot mixing rules for all atom pairs, except for those that are specified in the following variables.
          mixrule_adjust_total (integer)
            The number of pairs of atoms to set manually. This requires the following variables to be listed mixrule_adjust_total times.
              mixrule_adjust_key (character*10)
              • 'element': adjust any pair of nonbonded atom types that match the pair of element names.
              • 'nbname' adjust any pair of nonbonded atom types that match the pair of nonbonded names.
              mixrule_adjust_keynames (character*10 array)
                Character strings that are used to match according to the mixrule_adjust_key. These are listed on two lines, one line for each atom in the pair.
              mixrule_adjustments (double precision array)
                The values of the nonbonded coefficients to use for this pair of atoms instead of using the Lorentz-Berthelot combining rule. Units should be the same as normal for this type of classical_potential. In this case, that is Angstroms for σ and Kelvin for ε. You need to list four values, one per line: σ, ε, σ (1-4), and ε (1-4).
      lshift See the lshift section for information about this variable
      ltailc See the ltailc section for information about this variable
      rmin See the rmin section for information about this variable
      rcut See the rcut section for information about this variable
      rcutin See the rcutin section for information about this variable

  • 'Multiwell': multiple square wells and a hard sphere core
      Unonbond = infinity if r <= table_pair(1,1)
      Unonbond = table_pair(2,n) if table_pair(1,n-1) < r <= table_pair(1,n)
      Unonbond = 0 if table_pair(1,npair) < r
      classical_mixrule (character*30)
        This variable specifies the manner in which the parameters for unlike atoms are determined.
      • 'Lorentz-Berthelot': Arithmetic mean for the hard core and square well diameters. Geometric mean for the well depths.
      • 'Explicit': cross terms explicitly defined in the appropriate towhee_ff file.

  • 'Repulsive 2580 Multistep': Repulsive core multistep potential
      If the two atoms are separated by more than 3 bonds, or are on different molecules, then
      If r < nbcoeff(1)
        Unonbond = 1.0d10 * (nbcoeff(1)2 - r2)
      else if nbcoeff(1) <= r < 1.2 * nbcoeff(1)
        Unonbond = nbcoeff(2)
      else if 1.2 * nbcoeff(1) <= r < 1.5 * nbcoeff(1)
        Unonbond = nbcoeff(3)
      else if 1.5 * nbcoeff(1) <= r < 1.8 * nbcoeff(1)
        Unonbond = nbcoeff(4)
      else if 1.8 * nbcoeff(1) <= r < 2.0 * nbcoeff(1)
        Unonbond = nbcoeff(5)
      else if 2.0 * nbcoeff(1) <= r
        Unonbond = 0.0
      classical_mixrule (character*30)
        This variable specifies the manner in which the parameters for unlike atoms are determined.
      • 'Lorentz-Berthelot': arithmetic mean of σ, geometric mean of well depths.

  • 'Repulsive Multiwell': multiple square wells with a linear repulsive core
      Unonbond = 1.0d5 * (table_pair(1,1) - r) if r <= table_pair(1,1)
      Unonbond = table_pair(2,n) if table_pair(1,n-1) < r <= table_pair(1,n)
      Unonbond = 0 if table_pair(1,npair) < r
      classical_mixrule (character*30)
        This variable specifies the manner in which the parameters for unlike atoms are determined.
      • 'Lorentz-Berthelot': Arithmetic mean for the hard core and square well diameters. Geometric mean for the well depths.
      • 'Explicit': cross terms explicitly defined in the appropriate towhee_ff file.

  • 'Repulsive Sphere': This is used to help setup and equilibrate a hard sphere system where it is sometimes challenging to create an initial conformation with no overlaps. Use this option to equilibrate until the nonbonded potential energy is 0.0, and then switch back to the normal Hard Sphere potential.
      If the two atoms are separated by more than 3 bonds, or are on different molecules then
      Unonbond = 1d5 + 1d5 * (nbcoeff(1)^2 - r^2) if r <= nbcoeff(1), or 0 otherwise
      classical_mixrule (character*30)
        This variable specifies the manner in which the parameters for unlike atoms are determined.
      • 'Arithmetic': arithmetic mean of σ.

  • 'Repulsive Well': This is used to help setup and equilibrate a square well system where it is sometimes challenging to create an initial conformation with no overlaps. Use this option to equilibrate until the nonbonded potential energy is negative, and then switch back to the normal Square Well potential.
      Unonbond = 1 x 105 + 1 x 105 * ( nbcoeff(1)2 - r2 ) if r <= nbcoeff(1)
      Unonbond = -nbcoeff(3) if nbcoeff(1) < r <= nbcoeff(2)
      Unonbond = 0 if nbcoeff(2) < r
      classical_mixrule (character*30)
        This variable specifies the manner in which the parameters for unlike atoms are determined.
      • 'Lorentz-Berthelot': Arithmetic mean for the hard core and square well diameters. Geometric mean for the well depth.
      • 'Explicit': cross terms explicitly defined in the appropriate towhee_ff file.

  • 'Scaled Lennard-Jones': 12-6 Lennard-Jones potential with scaling of coulombic and van der Waals terms for selected atoms. Typically used for thermodynamic integration (see Beutler et al. and Shirts et al.).
      classical_mixrule (character*30)
        This variable specifies the manner in which the parameters for unlike atoms are determined.
      • 'Lorentz-Berthelot': arithmetic mean of σ, geometric mean of ε.
      • 'Geometric': geometric mean of σ and ε.
      • 'Explicit': cross terms explicitly specified in the appropriate towhee_ff file.
      • 'Shukla': complicated expression involving the polarizability of each atom. See equations 19 and 20 of Shukla 1987 for the definition of this mixing rule.
      cmix_rescaling_style (character*30)
        This variable controls the rescaling of the Lennard-Jones and coulombic potentials, typically used in thermodynamic integration calculations. It is valid only for the "Scaled Lennard-Jones" classical potential.
      • 'none': No additional adjustments to the nonbonded parameters as specified in the force field files and mixed according to the classical_mixrule. With this option, the potential is equivalent to the "Lennard-Jones" classical potential.
      • 'soft-core': The Lennard-Jones and coulombic components of intermolecular interactions are scaled by λLJ and λC parameters, respectively, as described in Shirts et al. 2003.

        The two-body potential between a scaled atom (as defined by cmix_pair_list, below) and an unscaled atom is given as,

          Utwo body = 4 * λLJ4 * ε * A (A - 1)
        where
          A-1 = αLJ * (1-λLJ)2 + (rij / σ)6
        For cases where neither, or both, atoms are scaled, the 'Lennard-Jones' classical potential is used. Note that for λLJ=1, this two-body term reduces to the 'Lennard-Jones' potential.

        Coulombic interactions are also scaled for the same set of atoms. Given a coulombic potential Ucoulomb between a scaled atom (as defined by cmix_pair_list, below) and an unscaled atom, the scaled coulomb potential is given as,
          U'coulomb = λC Ucoulomb
        At present, only coulombstyle of 'minimum image' is supported.

        The 'soft-core' cmix_rescaling_style option requires the following additional variables
          cmix_lambda_lj (double precision)
            The Lennard-Jones scaling factor λLJ. Require 0 ≤ cmix_lambda_lj ≤ 1.
          cmix_alpha_lj (double precision)
          cmix_lambda_c (double precision)
            The coulombic scaling factor λC. Require 0 ≤ cmix_lambda_c ≤ 1.
          cmix_lprintdudl (logical)
          • .TRUE. to evaluate and print ∂U/∂λLJ and ∂U/∂λC, the derivatives of the internal energy with respect to the two lambda parameters.
          • .FALSE. to ignore these calculations
          cmix_npair (integer)
            The number of atom types that are modified by this rescaling style. Must be positive.
          cmix_pair_list (character*10 array)
            The force field name and the atom type name for each value of cmix_npair. Listed with one force field name and atom type name per line.
      lshift See the lshift section for information about this variable
      rmin See the rmin section for information about this variable
      rcut See the rcut section for information about this variable
      rcutin See the rcutin section for information about this variable

  • 'Stillinger-Weber': Stillinger-Weber potential (see Stillinger and Weber 1985)
      This is an atomic potential and can only be used with monatomic molecules in Towhee
      U = nbcoeff(1)*[nbcoeff(2)*Sum u2(rij) + nbcoeff(7)*Sum u3(rij,rjk)]
      u2(rij) = [nbcoeff(3)*{rij/nbcoeff(4)}-nbcoeff(5) - 1] * exp{1/[(rij/nbcoeff(4) - nbcoeff(6))]} * Heaviside(nbcoeff(6) - [rij/nbcoeff(4)])
      u3(rij,rjk) = exp[ nbcoeff(8)/{rij/nbcoeff(4) - nbcoeff(6)} + nbcoeff(8)/{rjk/nbcoeff(4) - nbcoeff(6)}] * (cos(thetaijk)-nbcoeff(9))^2 * Heaviside(nbcoeff(6) - rij/nbcoeff(4)) * Heaviside(nbcoeff(6) - rjk/nbcoeff(4))
      classical_mixrule (character*30)
        This variable specifies the manner in which the parameters for unlike atoms are determined.
      • 'Explicit': cross terms explicitly defined in the appropriate towhee_ff file.

  • 'SW pair only': Stillinger-Weber potential (see Stillinger and Weber 1985) using only the pair potential
      This is an atomic potential and can only be used with monatomic molecules in Towhee. It is the same as the Stillinger-Weber potential but without the three-body terms that make it suitable for bonded materials. This option exists for academic study of the pair potential portion of the Stillinger-Weber functions. It reads from the same potential files as the 'Stillinger-Weber' potential.
      U = nbcoeff(1)*[nbcoeff(2)*Sum u2(rij)]
      u2(rij) = [nbcoeff(3)*{rij/nbcoeff(4)}-nbcoeff(5) - 1] * exp{1/[(rij/nbcoeff(4) - nbcoeff(6))]} * Heaviside(nbcoeff(6) - [rij/nbcoeff(4)])
      classical_mixrule (character*30)
        This variable specifies the manner in which the parameters for unlike atoms are determined.
      • 'Explicit': cross terms explicitly defined in the appropriate towhee_ff file.

  • 'Square Well': Square Well potential
      Unonbond = Infinity if r <= nbcoeff(1)
      Unonbond = -nbcoeff(3) if nbcoeff(1) < r <= nbcoeff(2)
      Unonbond = 0 if nbcoeff(2) < r
      classical_mixrule (character*30)
        This variable specifies the manner in which the parameters for unlike atoms are determined.
      • 'Lorentz-Berthelot': Arithmetic mean for the hard core and square well diameters. Geometric mean for the well depth.
      • 'Explicit': cross terms explicitly defined in the appropriate towhee_ff file.
      radial_pressure_delta See the radial_pressure_delta section for information about this variable

  • 'Tabulated Pair': Tabulated Pair Potential
      This potential uses a table to describe the interactions between atoms. The interpolatestyle determines the method for interpolating between the specified values of the pair potential terms. Cross terms between unlike atoms are described explicitly. The potential is listed with the distance and corresponding energy on each line.
      interpolatestyle See the interpolatestyle section for information about this variable

  • 'UFF 12-6': 12-6 potential with some additional nonbond coefficients.
      This uses the same parameters as the Lennard-Jones for computing the nonbonded interactions
      If the two atoms are separated by more than 3 bonds, or are on different molecules then
      Unonbond = 4 * nbcoeff(2) * [ (nbcoeff(1)/r)12 - (nbcoeff(1)/r)6 ]
      else if the two atoms are separated by exactly 3 bonds then
      Unonbond = 4 * nbcoeff(4) * [ (nbcoeff(3)/r)12 - (nbcoeff(3)/r)6 ]
      In addition, the following nbcoeff values are also stored. Some of these are required in order to compute the angle force constants.
      nbcoeff(5): valence bond length (UFF rI) in units of Angstroms.
      nbcoeff(6): valence bond angle (UFF theta0) in units of degrees.
      nbcoeff(7): nonbond distance (UFF xI) in units of Angstroms.
      nbcoeff(8): nonbond energy (UFF DI) in units of kcal/mol.
      nbcoeff(9): nonbond scale factor (UFF zeta) in arbitrary units.
      nbcoeff(10): effective charge (UFF ZI) in charge units.
      nbcoeff(11): electronegativity (UFF chiI) in eV.
      nbcoeff(12): torsion constant (UFF VI) in units of kcal/mol.
      classical_mixrule (character*30)
        This variable specifies the manner in which the parameters for unlike atoms are determined.
      • 'Geometric': geometric mean of σ and ε.
      lshift See the lshift section for information about this variable
      ltailc See the ltailc section for information about this variable
      rmin See the rmin section for information about this variable
      rcut See the rcut section for information about this variable
      rcutin See the rcutin section for information about this variable

  • 'Weeks-Chandler-Anderson': Repulsive-only version of 12-6 Lennard-Jones potential. See Weeks et al. 1970.
      This potential truncates the LJ potential for distances greater than the LJ minimum. The well depth is shifted by ε to make the remaining part all-repulsive. Useful for reference state calculations since the attractive part of LJ can be treated as a perturbation to the WCA repulsive-only potential.
      classical_mixrule (character*30)
        This variable specifies the manner in which the parameters for unlike atoms are determined.
      • 'Lorentz-Berthelot': arithmetic mean of σ, geometric mean of ε.
      • 'Geometric': geometric mean of σ and ε.
      • 'Explicit': cross terms explicitly specified in the appropriate towhee_ff file.
      • 'Shukla': complicated expression involving the polarizability of each atom. See equations 19 and 20 of Shukla 1987 for the definition of this mixing rule.
      cmix_rescaling_style (character*30)
        This variable controls the modification of the Lennard-Jones potential
      • 'none': No additional adjustments to the nonbonded parameters as specified in the force field files and mixed according to the classical_mixrule. With this option, the potential is equivalent to the "Lennard-Jones" classical potential.
      • 'WCA': Lennard-Jones interactions are modified as in Weeks et al. 1970.
        The potential between a modified atom (as defined by cmix_pair_list below) and any other atom less than 21/6 * nbcoeff(1) away is:
          Unonbond = 4 * nbcoeff(2) * [ (nbcoeff(1)/r)12 - (nbcoeff(1)/r)6 ] + nbcoeff(2)
        If the interatomic distance is greater than or equal to 21/6 * nbcoeff(1) then:
          Unonbond = 0
        For cases where neither atom is scaled, the 'Lennard-Jones' classical potential is used.
        This option requires the following additional variables
          cmix_npair (integer)
            The number of atom types that are modified by this rescaling style. Must be positive.
          cmix_pair_list (character*10 array)
            The force field name and the atom type name for each value of cmix_npair. Listed with one force field name and atom type name per line.
          lshift See the lshift section for information about this variable
          rmin See the rmin section for information about this variable
          rcut See the rcut section for information about this variable
          rcutin See the rcutin section for information about this variable

  • This section contains a description of variables that are identical in meaning regardless of the value of classical_potential. Please note that not all of these variables are required for each value of the classical_potential so you should consult the information above to determine which are required.
      lshift (logical)
      • .true. if you want the nonbonded potential to be shifted so that it is zero at the cutoff.
      • .false. if you do not want to shift the nonbonded potential.
      ltailc (logical)
      • .true. if you want to apply analytical tail corrections for the portion of the potential that is past the cutoff. Note that you cannot have a shifted potential and tail corrections at the same time.
      • .false. if you do not want analytical tail corrections.
      rmin (double precision)
      • A hard inner cutoff that can speed computation for Lennard-Jones systems, and is required to avoid the potential hitting infinity for exponential repulsion systems which also contain point charges. This should be set smaller than the smallest radius of any atom. The suggested default values are in the range from 0.5 to 1.0 Angstroms.
      rcut (double precision)
      • The distance (in Angstroms) beyond which the nonbonded potential (and density potential in the case of Embedded Atom Method) are no longer computed. This has no effect upon the coulombic potential as that is controlled by the coulombstyle variables. The rcut variable is also used to determine where to shift the potential (if lshift is true) or where to begin applying long range tail corrections (if ltailc is true). Note that this value is automatically adjusted upwards for certain types of Embedded Atom Method potentials.
      rcutin (double precision)
      • The inner nonbonded cutoff used in configurational-bias Monte Carlo moves. This dual-cutoff method can speed configurational-bias computations by at least a factor of 2, without affecting the acceptance rate. The inner cutoff is used during the growth procedure, and the full potential is calculated at the end of the move and everything is fixed up in the acceptance criteria. Suggested default values are 5 Angstroms for noncoulombic simulations, and 10 Angstroms for coulombic simulations.
      interpolatestyle (character*20)
      • 'cubicspline': Uses a cubic spline to interpolate between the tabulated portion of the force field data points provided in the force field files.
      • 'linear': Linear interpolation between the data points of the tabulated portion of the force field
      radial_pressure_delta (double precision)
        This variable specifies the bin width that is used to compute local radial distribution functions near the discontinuities in the potential in order to calculate the pressure of the system. In general, setting this as close to zero as possible reduces the systematic errors of the method. However, as this setting gets very small the sampling becomes more difficult and the statistical errors become large. Please see the Towhee standard output manual for more information about the Radial pressure. The currently recommended default value is 1.0d-2.
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Last updated: July 19, 2013