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tim |
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// This is the forcefield file for the Dipolar Unified-atom Force Field (DUFF). |
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// |
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// The sections are divided into AtomTypes, BondTypes, BendTypes, |
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// and TorsionTypes. |
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// |
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// Many parameters (but not all) are derived from the TRAPPE force field |
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// of Siepmann's group. |
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begin AtomTypes |
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//AtomTypeName isDirectional isLJ isCharge mass (amu) epsilon (kcal/mol) sigma (Ang) q (e) |
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CH4 0 1 0 16.05 0.279 3.73 |
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CH3 0 1 0 15.04 0.185 3.75 |
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CH2 0 1 0 14.03 0.0866 3.95 |
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CH 0 1 0 13.02 0.0189 4.68 |
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SSD 1 1 0 18.0153 0.152 3.035 |
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HEAD 1 1 0 196 0.185 5.75 |
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TB1 0 1 0 14.03 0.0866 4.0 |
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TE1 0 1 0 15.04 0.185 4.0 |
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TB2 0 1 0 21.05 0.25 6.0 |
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TE2 0 1 0 22.56 0.5 6.0 |
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TB3 0 1 0 28.06 0.5 8.0 |
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TE3 0 1 0 30.08 0.75 8.0 |
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end AtomTypes |
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begin DirectionalAtomType |
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//AtomTypeName isDipole isSticky I_xx (amu*Ang^2) I_yy I_zz dipole (Debye) w0 v0 (kcal/mol) v0p rl (Ang) ru rlp rup |
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SSD 1 1 1.7696 0.6145 1.1550 2.35 0.07715 3.7284 3.7284 2.75 3.35 2.75 4.0 |
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HEAD 1 0 1125 1125 250 20.6 |
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end DirectionalAtomType |
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begin BondTypes |
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//Atom1 Atom2 FixedBondType |
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//V_FixedBondType = 0 |
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//Atom1 Atom2 HarmonicBondType b0 Kb (kcal/mol) |
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//V_HarmonicBondType = Kb(b- bo)^2 |
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//HarmonicBondType Examples |
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HEAD CH3 HarmonicBondType 2.75 260 |
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HEAD CH2 HarmonicBondType 2.75 260 |
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HEAD CH HarmonicBondType 2.75 260 |
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HEAD TB1 HarmonicBondType 2.76 260 |
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HEAD TB2 HarmonicBondType 3.20 260 |
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HEAD TB3 HarmonicBondType 3.63 260 |
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CH3 CH3 HarmonicBondType 1.526 260 |
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CH3 CH2 HarmonicBondType 1.526 260 |
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CH3 CH HarmonicBondType 1.526 260 |
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CH2 CH2 HarmonicBondType 1.526 260 |
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CH2 CH HarmonicBondType 1.526 260 |
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CH CH HarmonicBondType 1.526 260 |
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TB1 TB1 HarmonicBondType 1.526 260 |
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TB2 TB2 HarmonicBondType 2.34 260 |
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TB3 TB3 HarmonicBondType 3.12 260 |
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TB1 TE1 HarmonicBondType 1.526 260 |
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TB2 TE2 HarmonicBondType 2.34 260 |
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TB3 TE3 HarmonicBondType 3.12 260 |
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//Atom1 Atom2 CubicBondType b0 K3 K2 K1 K0 |
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//V_CubicBondType = K3(b - b0)^3 + K2(b - b0)^2 + K1(b - b0) + K0 |
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//Atom1 Atom2 QuadraticBondType b0 K4 K3 K2 K1 K0 |
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//V_QuadraticBondType = K4(b - b0)^4 + K3(b - b0)^3 + K2(b - b0)^2 + K1(b - b0) + K0 |
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//Atom1 Atom2 PolynomialBondType b0 i Ki [j Kj] |
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//V_QuadraticBondType = Ki(b - b0)^i + Kj(b - b0)^j + ... |
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end BondTypes |
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begin BendTypes |
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//HarmonicBendType |
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//Atom1 Atom2 Atom3 HarmonicBendType Ktheta Theta0 |
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//V_HarmonicBendType = Ktheta(Theta - Theta0)^2 |
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//Ktheta: kcal/mole/rad**2 |
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//Theta0: degrees |
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//HarmonicBendType examples |
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HEAD CH2 HEAD HarmonicBendType 58.84 114.0 |
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HEAD CH2 CH3 HarmonicBendType 58.84 114.0 |
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HEAD CH2 CH2 HarmonicBendType 58.84 114.0 |
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HEAD TB1 TB1 HarmonicBendType 58.84 114.0 |
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HEAD TB2 TB2 HarmonicBendType 58.84 114.0 |
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HEAD TB3 TB3 HarmonicBendType 58.84 114.0 |
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HEAD CH2 CH HarmonicBendType 58.84 114.0 |
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HEAD CH CH3 HarmonicBendType 58.84 112.0 |
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HEAD CH CH2 HarmonicBendType 58.84 112.0 |
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HEAD CH CH HarmonicBendType 58.84 112.0 |
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CH3 CH2 CH3 HarmonicBendType 58.84 114.0 |
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CH3 CH2 CH2 HarmonicBendType 58.84 114.0 |
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CH3 CH2 CH HarmonicBendType 58.84 114.0 |
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CH3 CH CH3 HarmonicBendType 58.84 112.0 |
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CH3 CH CH2 HarmonicBendType 58.84 112.0 |
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CH3 CH CH HarmonicBendType 58.84 112.0 |
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CH2 CH2 CH2 HarmonicBendType 58.84 114.0 |
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CH2 CH2 CH HarmonicBendType 58.84 114.0 |
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CH2 CH CH2 HarmonicBendType 58.84 112.0 |
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CH2 CH CH HarmonicBendType 58.84 112.0 |
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CH CH2 CH HarmonicBendType 58.84 114.0 |
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CH CH CH HarmonicBendType 58.84 112.0 |
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TB1 TB1 TB1 HarmonicBendType 58.84 114.0 |
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TB2 TB2 TB2 HarmonicBendType 58.84 114.0 |
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TB3 TB3 TB3 HarmonicBendType 58.84 114.0 |
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TE1 TB1 TB1 HarmonicBendType 58.84 114.0 |
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TE2 TB2 TB2 HarmonicBendType 58.84 114.0 |
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TE3 TB3 TB3 HarmonicBendType 58.84 114.0 |
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//GhostBend |
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//Atom1 Atom2 GHOST GhostBendType Ktheta Theta0 |
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//Atom2 must be directional atom |
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//GhostBendType examples |
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CH2 HEAD GHOST GhostBendType 0.00176972 129.783 |
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CH2 HEAD GHOST GhostBendType 58.84 90.0 |
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TB1 HEAD GHOST GhostBendType 58.84 90.0 |
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TB2 HEAD GHOST GhostBendType 58.84 90.0 |
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TB3 HEAD GHOST GhostBendType 58.84 90.0 |
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//UreyBradleyBend |
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//Atom1 Atom2 Atom3 UreyBradleyBend Ktheta Theta0 Kub S0 |
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//V_UreyBradleyBend = Ktheta(Theta - Theta0)^2 + Kub(S - S0)^2 |
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//Ktheta: kcal/mole/rad**2 |
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//Theta0: degrees |
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//Kub: kcal/mole/A**2 |
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//S0: A |
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//CubicBendType |
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//Atom1 Atom2 Atom3 CubicBendType Theta0 K3 K2 K1 K0 |
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//V_CubicBendType = K3(Theta - Theta0)^3 + K2(Theta - Theta0)^2 + K1(Theta - Theta0) + K0 |
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//QuadraticBendType |
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//Atom1 Atom2 Atom3 QuadraticBendType Theta0 K4 K3 K2 K1 K0 |
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//V_QuadraticBendType = K4(Theta - Theta0)^4 + K3(Theta - Theta0)^3 + K2(Theta - Theta0)^2 + K1(Theta - Theta0) + K0 |
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//PolynomialBendType |
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//Atom1 Atom2 Atom3 PolynomialBendType Theta0 i Ki [j Kj] |
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//V_PolynomialBendType = Ki(Theta - Theta0)^i + Kj(Theta - Theta0)^j + ... |
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end BendTypes |
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begin TorsionTypes |
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//CubicTorsionType |
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//Atom1 Atom2 Atom3 Atom4 CubicTorsionType k3 k2 k1 k0 ( all are kcal/mol ) |
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//V_CubicTorsionType = k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0 |
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//CubicTorsionType Examples |
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HEAD CH2 CH2 HEAD CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
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HEAD CH2 CH HEAD CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
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HEAD CH CH HEAD CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
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HEAD CH2 CH2 CH3 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
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HEAD CH2 CH CH3 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
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HEAD CH CH2 CH3 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
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HEAD CH CH CH3 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
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HEAD CH2 CH2 CH2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
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HEAD CH2 CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
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HEAD CH CH2 CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
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HEAD CH CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
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HEAD CH2 CH2 CH CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
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HEAD CH2 CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
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HEAD CH CH2 CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
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HEAD CH CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
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HEAD TB1 TB1 TB1 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
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HEAD TB2 TB2 TB2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
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HEAD TB3 TB3 TB3 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
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CH3 CH2 CH2 CH3 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
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CH3 CH2 CH CH3 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
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CH3 CH CH CH3 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
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CH3 CH2 CH2 CH2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
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CH3 CH2 CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
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CH3 CH CH2 CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
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CH3 CH CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
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CH3 CH2 CH2 CH CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
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CH3 CH2 CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
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CH3 CH CH2 CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
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CH3 CH CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
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CH2 CH2 CH2 CH2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
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CH2 CH2 CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
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CH2 CH CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
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CH2 CH2 CH2 CH CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
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CH2 CH2 CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
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CH2 CH CH2 CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
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CH2 CH CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
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CH CH2 CH2 CH CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
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CH CH2 CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
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CH CH CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
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TB1 TB1 TB1 TB1 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
| 363 |
|
|
|
| 364 |
|
|
TB2 TB2 TB2 TB2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
| 365 |
|
|
|
| 366 |
|
|
TB3 TB3 TB3 TB3 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
| 367 |
|
|
|
| 368 |
|
|
TE1 TB1 TB1 TB1 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
| 369 |
|
|
|
| 370 |
|
|
TE2 TB2 TB2 TB2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
| 371 |
|
|
|
| 372 |
|
|
TE3 TB3 TB3 TB3 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
| 373 |
|
|
|
| 374 |
|
|
|
| 375 |
|
|
|
| 376 |
|
|
//CharmmTorsionType |
| 377 |
|
|
|
| 378 |
|
|
//Atom1 Atom2 Atom3 Atom4 CharmmTorsionType Kchi n delta [Kchi n delta] |
| 379 |
|
|
|
| 380 |
|
|
//V_CharmmTorsionType = Kchi(1 + cos(n(chi) - delta)) |
| 381 |
|
|
|
| 382 |
|
|
//Kchi: kcal/mole |
| 383 |
|
|
|
| 384 |
|
|
//n: multiplicity |
| 385 |
|
|
|
| 386 |
|
|
//delta: degrees |
| 387 |
|
|
|
| 388 |
|
|
//in some cases, a CharmmTorsionType may have two or three terms. If n is equal to 0, it falls back to harmonic form |
| 389 |
|
|
|
| 390 |
|
|
|
| 391 |
|
|
|
| 392 |
|
|
//QuadraticTorsionType |
| 393 |
|
|
|
| 394 |
|
|
//Atom1 Atom2 Atom3 Atom4 QuadraticTorsionType k4 k3 k2 k1 k0 ( all are kcal/mol ) |
| 395 |
|
|
|
| 396 |
|
|
//V_QuadraticTorsionType = k4(cos phi)^4 + k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0 |
| 397 |
|
|
|
| 398 |
|
|
|
| 399 |
|
|
|
| 400 |
|
|
//PolynomialTorsionType |
| 401 |
|
|
|
| 402 |
|
|
//Atom1 Atom2 Atom3 Atom4 PolynomialTorsionType i Ki [j Kj] |
| 403 |
|
|
|
| 404 |
|
|
//VPolynomialTorsionType = Ki (cos phi)^i + ... + Kj (cos phi)^j |
| 405 |
|
|
|
| 406 |
|
|
|
| 407 |
|
|
|
| 408 |
tim |
1755 |
end TorsionTypes |
