| 1 |
// This is the forcefield file for the Dipolar Unified-atom Force Field (DUFF).
|
| 2 |
//
|
| 3 |
// The sections are divided into AtomTypes, BondTypes, BendTypes,
|
| 4 |
// and TorsionTypes.
|
| 5 |
//
|
| 6 |
// Many parameters (but not all) are derived from the TRAPPE force field
|
| 7 |
// of Siepmann's group.
|
| 8 |
|
| 9 |
begin AtomTypes
|
| 10 |
//Atom isDipole isSSD mass LJ epsilon ( kcal/mol) LJ sigma (Angstroms) Dipole Moment (Debye) w0 v0 (kcal/mol) v0p (kcal/mol) rl (Angstroms) ru (Angstroms) rlp (Angstroms) rup (Angstroms)
|
| 11 |
|
| 12 |
CH4 0 0 16.05 0.279 3.73
|
| 13 |
CH3 0 0 15.04 0.185 3.75
|
| 14 |
CH2 0 0 14.03 0.0866 3.95
|
| 15 |
CH 0 0 13.02 0.0189 4.68
|
| 16 |
SSD 1 1 18.0153 0.152 3.035 2.42 0.07715 3.9 3.9 2.4 3.8 2.75 3.35
|
| 17 |
HEAD 1 0 196 0.185 5.75 20.6
|
| 18 |
TB1 0 0 14.03 0.0866 4.0
|
| 19 |
TE1 0 0 15.04 0.185 4.0
|
| 20 |
TB2 0 0 21.05 0.25 6.0
|
| 21 |
TE2 0 0 22.56 0.5 6.0
|
| 22 |
TB3 0 0 28.06 0.5 8.0
|
| 23 |
TE3 0 0 30.08 0.75 8.0
|
| 24 |
|
| 25 |
end AtomTypes
|
| 26 |
|
| 27 |
begin BondTypes
|
| 28 |
|
| 29 |
//Atom1 Atom2 FixedBondType
|
| 30 |
//V_FixedBondType = 0
|
| 31 |
|
| 32 |
//Atom1 Atom2 HarmonicBondType b0 Kb (kcal/mol)
|
| 33 |
//V_HarmonicBondType = Kb(b- bo)^2
|
| 34 |
//HarmonicBondType Examples
|
| 35 |
HEAD CH3 HarmonicBondType 2.75 260
|
| 36 |
HEAD CH2 HarmonicBondType 2.75 260
|
| 37 |
HEAD CH HarmonicBondType 2.75 260
|
| 38 |
HEAD TB1 HarmonicBondType 2.76 260
|
| 39 |
HEAD TB2 HarmonicBondType 3.20 260
|
| 40 |
HEAD TB3 HarmonicBondType 3.63 260
|
| 41 |
CH3 CH3 HarmonicBondType 1.526 260
|
| 42 |
CH3 CH2 HarmonicBondType 1.526 260
|
| 43 |
CH3 CH HarmonicBondType 1.526 260
|
| 44 |
CH2 CH2 HarmonicBondType 1.526 260
|
| 45 |
CH2 CH HarmonicBondType 1.526 260
|
| 46 |
CH CH HarmonicBondType 1.526 260
|
| 47 |
TB1 TB1 HarmonicBondType 1.526 260
|
| 48 |
TB2 TB2 HarmonicBondType 2.34 260
|
| 49 |
TB3 TB3 HarmonicBondType 3.12 260
|
| 50 |
TB1 TE1 HarmonicBondType 1.526 260
|
| 51 |
TB2 TE2 HarmonicBondType 2.34 260
|
| 52 |
TB3 TE3 HarmonicBondType 3.12 260
|
| 53 |
|
| 54 |
//Atom1 Atom2 CubicBondType b0 K3 K2 K1 K0
|
| 55 |
//V_CubicBondType = K3(b - b0)^3 + K2(b - b0)^2 + K1(b - b0) + K0
|
| 56 |
|
| 57 |
|
| 58 |
//Atom1 Atom2 QuadraticBondType b0 K4 K3 K2 K1 K0
|
| 59 |
//V_QuadraticBondType = K4(b - b0)^4 + K3(b - b0)^3 + K2(b - b0)^2 + K1(b - b0) + K0
|
| 60 |
|
| 61 |
|
| 62 |
//Atom1 Atom2 PolynomialBondType b0 i Ki [j Kj]
|
| 63 |
//V_QuadraticBondType = Ki(b - b0)^i + Kj(b - b0)^j + ...
|
| 64 |
|
| 65 |
|
| 66 |
end BondTypes
|
| 67 |
|
| 68 |
begin BendTypes
|
| 69 |
|
| 70 |
//HarmonicBendType
|
| 71 |
//Atom1 Atom2 Atom3 HarmonicBendType Ktheta Theta0
|
| 72 |
//V_HarmonicBendType = Ktheta(Theta - Theta0)^2
|
| 73 |
//Ktheta: kcal/mole/rad**2
|
| 74 |
//Theta0: degrees
|
| 75 |
//HarmonicBendType examples
|
| 76 |
HEAD CH2 HEAD HarmonicBendType 58.84 114.0
|
| 77 |
HEAD CH2 CH3 HarmonicBendType 58.84 114.0
|
| 78 |
HEAD CH2 CH2 HarmonicBendType 58.84 114.0
|
| 79 |
HEAD TB1 TB1 HarmonicBendType 58.84 114.0
|
| 80 |
HEAD TB2 TB2 HarmonicBendType 58.84 114.0
|
| 81 |
HEAD TB3 TB3 HarmonicBendType 58.84 114.0
|
| 82 |
HEAD CH2 CH HarmonicBendType 58.84 114.0
|
| 83 |
HEAD CH CH3 HarmonicBendType 58.84 112.0
|
| 84 |
HEAD CH CH2 HarmonicBendType 58.84 112.0
|
| 85 |
HEAD CH CH HarmonicBendType 58.84 112.0
|
| 86 |
CH3 CH2 CH3 HarmonicBendType 58.84 114.0
|
| 87 |
CH3 CH2 CH2 HarmonicBendType 58.84 114.0
|
| 88 |
CH3 CH2 CH HarmonicBendType 58.84 114.0
|
| 89 |
CH3 CH CH3 HarmonicBendType 58.84 112.0
|
| 90 |
CH3 CH CH2 HarmonicBendType 58.84 112.0
|
| 91 |
CH3 CH CH HarmonicBendType 58.84 112.0
|
| 92 |
CH2 CH2 CH2 HarmonicBendType 58.84 114.0
|
| 93 |
CH2 CH2 CH HarmonicBendType 58.84 114.0
|
| 94 |
CH2 CH CH2 HarmonicBendType 58.84 112.0
|
| 95 |
CH2 CH CH HarmonicBendType 58.84 112.0
|
| 96 |
CH CH2 CH HarmonicBendType 58.84 114.0
|
| 97 |
CH CH CH HarmonicBendType 58.84 112.0
|
| 98 |
TB1 TB1 TB1 HarmonicBendType 58.84 114.0
|
| 99 |
TB2 TB2 TB2 HarmonicBendType 58.84 114.0
|
| 100 |
TB3 TB3 TB3 HarmonicBendType 58.84 114.0
|
| 101 |
TE1 TB1 TB1 HarmonicBendType 58.84 114.0
|
| 102 |
TE2 TB2 TB2 HarmonicBendType 58.84 114.0
|
| 103 |
TE3 TB3 TB3 HarmonicBendType 58.84 114.0
|
| 104 |
|
| 105 |
//GhostBend
|
| 106 |
//Atom1 Atom2 GHOST GhostBendType Ktheta Theta0
|
| 107 |
//Atom2 must be directional atom
|
| 108 |
//GhostBendType examples
|
| 109 |
CH2 HEAD GHOST GhostBendType 0.00176972 129.783
|
| 110 |
CH2 HEAD GHOST GhostBendType 58.84 90.0
|
| 111 |
TB1 HEAD GHOST GhostBendType 58.84 90.0
|
| 112 |
TB2 HEAD GHOST GhostBendType 58.84 90.0
|
| 113 |
TB3 HEAD GHOST GhostBendType 58.84 90.0
|
| 114 |
|
| 115 |
//UreyBradleyBend
|
| 116 |
//Atom1 Atom2 Atom3 UreyBradleyBend Ktheta Theta0 Kub S0
|
| 117 |
//V_UreyBradleyBend = Ktheta(Theta - Theta0)^2 + Kub(S - S0)^2
|
| 118 |
//Ktheta: kcal/mole/rad**2
|
| 119 |
//Theta0: degrees
|
| 120 |
//Kub: kcal/mole/A**2
|
| 121 |
//S0: A
|
| 122 |
|
| 123 |
//CubicBendType
|
| 124 |
//Atom1 Atom2 Atom3 CubicBendType Theta0 K3 K2 K1 K0
|
| 125 |
//V_CubicBendType = K3(Theta - Theta0)^3 + K2(Theta - Theta0)^2 + K1(Theta - Theta0) + K0
|
| 126 |
|
| 127 |
//QuadraticBendType
|
| 128 |
//Atom1 Atom2 Atom3 QuadraticBendType Theta0 K4 K3 K2 K1 K0
|
| 129 |
//V_QuadraticBendType = K4(Theta - Theta0)^4 + K3(Theta - Theta0)^3 + K2(Theta - Theta0)^2 + K1(Theta - Theta0) + K0
|
| 130 |
|
| 131 |
//PolynomialBendType
|
| 132 |
//Atom1 Atom2 Atom3 PolynomialBendType Theta0 i Ki [j Kj]
|
| 133 |
//V_PolynomialBendType = Ki(Theta - Theta0)^i + Kj(Theta - Theta0)^j + ...
|
| 134 |
|
| 135 |
end BendTypes
|
| 136 |
|
| 137 |
begin TorsionTypes
|
| 138 |
|
| 139 |
//CubicTorsionType
|
| 140 |
//Atom1 Atom2 Atom3 Atom4 CubicTorsionType k3 k2 k1 k0 ( all are kcal/mol )
|
| 141 |
//V_CubicTorsionType = k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0
|
| 142 |
//CubicTorsionType Examples
|
| 143 |
HEAD CH2 CH2 HEAD CubicTorsionType 5.9602 -0.2568 -3.802 2.1586
|
| 144 |
HEAD CH2 CH HEAD CubicTorsionType 3.3254 -0.4215 -1.686 1.1661
|
| 145 |
HEAD CH CH HEAD CubicTorsionType 3.3254 -0.4215 -1.686 1.1661
|
| 146 |
HEAD CH2 CH2 CH3 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586
|
| 147 |
HEAD CH2 CH CH3 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661
|
| 148 |
HEAD CH CH2 CH3 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661
|
| 149 |
HEAD CH CH CH3 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661
|
| 150 |
HEAD CH2 CH2 CH2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586
|
| 151 |
HEAD CH2 CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661
|
| 152 |
HEAD CH CH2 CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661
|
| 153 |
HEAD CH CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661
|
| 154 |
HEAD CH2 CH2 CH CubicTorsionType 5.9602 -0.2568 -3.802 2.1586
|
| 155 |
HEAD CH2 CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661
|
| 156 |
HEAD CH CH2 CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661
|
| 157 |
HEAD CH CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661
|
| 158 |
HEAD TB1 TB1 TB1 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586
|
| 159 |
HEAD TB2 TB2 TB2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586
|
| 160 |
HEAD TB3 TB3 TB3 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586
|
| 161 |
CH3 CH2 CH2 CH3 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586
|
| 162 |
CH3 CH2 CH CH3 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661
|
| 163 |
CH3 CH CH CH3 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661
|
| 164 |
CH3 CH2 CH2 CH2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586
|
| 165 |
CH3 CH2 CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661
|
| 166 |
CH3 CH CH2 CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661
|
| 167 |
CH3 CH CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661
|
| 168 |
CH3 CH2 CH2 CH CubicTorsionType 5.9602 -0.2568 -3.802 2.1586
|
| 169 |
CH3 CH2 CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661
|
| 170 |
CH3 CH CH2 CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661
|
| 171 |
CH3 CH CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661
|
| 172 |
CH2 CH2 CH2 CH2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586
|
| 173 |
CH2 CH2 CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661
|
| 174 |
CH2 CH CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661
|
| 175 |
CH2 CH2 CH2 CH CubicTorsionType 5.9602 -0.2568 -3.802 2.1586
|
| 176 |
CH2 CH2 CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661
|
| 177 |
CH2 CH CH2 CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661
|
| 178 |
CH2 CH CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661
|
| 179 |
CH CH2 CH2 CH CubicTorsionType 5.9602 -0.2568 -3.802 2.1586
|
| 180 |
CH CH2 CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661
|
| 181 |
CH CH CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661
|
| 182 |
TB1 TB1 TB1 TB1 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586
|
| 183 |
TB2 TB2 TB2 TB2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586
|
| 184 |
TB3 TB3 TB3 TB3 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586
|
| 185 |
TE1 TB1 TB1 TB1 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586
|
| 186 |
TE2 TB2 TB2 TB2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586
|
| 187 |
TE3 TB3 TB3 TB3 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586
|
| 188 |
|
| 189 |
//CharmmTorsionType
|
| 190 |
//Atom1 Atom2 Atom3 Atom4 CharmmTorsionType Kchi n delta [Kchi n delta]
|
| 191 |
//V_CharmmTorsionType = Kchi(1 + cos(n(chi) - delta))
|
| 192 |
//Kchi: kcal/mole
|
| 193 |
//n: multiplicity
|
| 194 |
//delta: degrees
|
| 195 |
//in some cases, a CharmmTorsionType may have two or three terms. If n is equal to 0, it falls back to harmonic form
|
| 196 |
|
| 197 |
//QuadraticTorsionType
|
| 198 |
//Atom1 Atom2 Atom3 Atom4 QuadraticTorsionType k4 k3 k2 k1 k0 ( all are kcal/mol )
|
| 199 |
//V_QuadraticTorsionType = k4(cos phi)^4 + k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0
|
| 200 |
|
| 201 |
//PolynomialTorsionType
|
| 202 |
//Atom1 Atom2 Atom3 Atom4 PolynomialTorsionType i Ki [j Kj]
|
| 203 |
//VPolynomialTorsionType = Ki (cos phi)^i + ... + Kj (cos phi)^j
|
| 204 |
|
| 205 |
end TorsionTypes |
