| 1 |
// This is the forcefield file for the Metal-NonMetal(MnM) Interaction Forcefield |
| 2 |
// |
| 3 |
// The sections are divided into AtomTypes |
| 4 |
// |
| 5 |
|
| 6 |
|
| 7 |
begin Options |
| 8 |
Name = "MnM" |
| 9 |
MetallicEnergyUnitScaling 23.0605423 |
| 10 |
end Options |
| 11 |
|
| 12 |
begin AtomTypes |
| 13 |
//Name mass (amu) |
| 14 |
CH4 16.05 |
| 15 |
CH3 15.04 |
| 16 |
CH2 14.03 |
| 17 |
CH 13.02 |
| 18 |
thCH3 15.04 |
| 19 |
thCH2 14.03 |
| 20 |
//thS 32.0655 |
| 21 |
SSD 18.0153 |
| 22 |
SSD1 18.0153 |
| 23 |
SSD_E 18.0153 |
| 24 |
SSD_RF 18.0153 |
| 25 |
O_TIP3P 15.9994 |
| 26 |
O_TIP4P 15.9994 |
| 27 |
O_TIP4P-Ew 15.9994 |
| 28 |
O_TIP5P 15.9994 |
| 29 |
O_TIP5P-E 15.9994 |
| 30 |
O_SPCE 15.9994 |
| 31 |
O_SPC 15.9994 |
| 32 |
H_TIP3P 1.0079 |
| 33 |
H_TIP4P 1.0079 |
| 34 |
H_TIP4P-Ew 1.0079 |
| 35 |
H_TIP5P 1.0079 |
| 36 |
H_SPCE 1.0079 |
| 37 |
H_SPC 1.0079 |
| 38 |
EP_TIP4P 0.0 |
| 39 |
EP_TIP4P-Ew 0.0 |
| 40 |
EP_TIP5P 0.0 |
| 41 |
C 12.0107 |
| 42 |
S 32.0655 |
| 43 |
Ni 58.710 |
| 44 |
Cu 63.550 |
| 45 |
Rh 102.90550 |
| 46 |
Pd 106.42 |
| 47 |
Ag 107.8682 |
| 48 |
Ir 192.217 |
| 49 |
Pt 195.09 |
| 50 |
Au 196.97 |
| 51 |
end AtomTypes |
| 52 |
|
| 53 |
begin DirectionalAtomTypes |
| 54 |
//Name I_xx I_yy I_zz (All moments in (amu*Ang^2) |
| 55 |
SSD 1.7696 0.6145 1.1550 |
| 56 |
SSD1 1.7696 0.6145 1.1550 |
| 57 |
SSD_E 1.7696 0.6145 1.1550 |
| 58 |
SSD_RF 1.7696 0.6145 1.1550 |
| 59 |
end DirectionalAtomTypes |
| 60 |
|
| 61 |
|
| 62 |
begin LennardJonesAtomTypes |
| 63 |
//Name epsilon sigma |
| 64 |
SSD 0.152 3.051 |
| 65 |
SSD1 0.152 3.016 |
| 66 |
SSD_E 0.152 3.035 |
| 67 |
SSD_RF 0.152 3.019 |
| 68 |
O_TIP3P 0.1521 3.15061 |
| 69 |
O_TIP4P 0.1550 3.15365 |
| 70 |
O_TIP4P-Ew 0.16275 3.16435 |
| 71 |
O_TIP5P 0.16 3.12 |
| 72 |
O_TIP5P-E 0.178 3.097 |
| 73 |
O_SPCE 0.15532 3.16549 |
| 74 |
O_SPC 0.15532 3.16549 |
| 75 |
CH4 0.279 3.73 |
| 76 |
//CH3 0.185 3.75 |
| 77 |
//CH2 0.0866 3.95 |
| 78 |
CH 0.0189 4.68 |
| 79 |
C 0.101745452544 3.35 |
| 80 |
CH3 0.2146 3.76 |
| 81 |
CH2 0.1127 3.96 |
| 82 |
S 0.2504 4.45 |
| 83 |
end LennardJonesAtomTypes |
| 84 |
|
| 85 |
begin SCAtomTypes |
| 86 |
// Name epsilon(eV) c m n alpha(angstroms) |
| 87 |
Ni 0.0073767 84.745 5.0 10.0 3.5157 |
| 88 |
Cu 0.0057921 84.843 5.0 10.0 3.6030 |
| 89 |
Rh 0.0024612 305.499 5.0 13.0 3.7984 |
| 90 |
Pd 0.0032864 148.205 6.0 12.0 3.8813 |
| 91 |
Ag 0.0039450 96.524 6.0 11.0 4.0691 |
| 92 |
Ir 0.0037674 224.815 6.0 13.0 3.8344 |
| 93 |
Pt 0.0097894 71.336 7.0 11.0 3.9163 |
| 94 |
Au 0.0078052 53.581 8.0 11.0 4.0651 |
| 95 |
end SCAtomTypes |
| 96 |
|
| 97 |
|
| 98 |
// Metal non-metal interactions. |
| 99 |
// Format: Metal Atom Type, Non-Metal Atom Type, Interaction Type, Interaction Parameters |
| 100 |
// Where interaction type can be: MAW, LennardJones or ShiftedMorse or RepulsiveMorse |
| 101 |
begin MetalNonMetalInteractions |
| 102 |
|
| 103 |
//MAW (Metal Angular Water section) |
| 104 |
// r_e, D_e beta ca1 cb1 |
| 105 |
Cu SSD_E MAW 2.5525 1.9850 1.1680 1.1250 0.750000 |
| 106 |
//Au SSD_E MAW 2.8170 1.7850 1.2680 1.2500 0.2050 0.0 |
| 107 |
//Au SSD_E MAW 2.7510 2.95 1.101 0.750000 0.750000 |
| 108 |
//1. 1.5 2.6500001 -3.000162356E-2 1.30999744 |
| 109 |
//Au SSD_E MAW 2.7 1.06 1.264 0.16 0.8 |
| 110 |
Au SSD_E MAW 2.68 0.6 1.33 0.95 -0.25 |
| 111 |
|
| 112 |
//LennardJones |
| 113 |
// sigma epsilon |
| 114 |
Au CH3 LennardJones 3.54 0.2146 |
| 115 |
Au CH2 LennardJones 3.54 0.1749 |
| 116 |
Au S LennardJones 4.45 9.180 |
| 117 |
|
| 118 |
//Shifted Morse |
| 119 |
// r0 D0 beta0 |
| 120 |
Au O_SPCE ShiftedMorse 3.70 0.0424 0.769 |
| 121 |
|
| 122 |
//Repulsive Morse |
| 123 |
// r0 D0 beta0 |
| 124 |
Au H_SPCE RepulsiveMorse -1.00 0.00850 0.769 |
| 125 |
|
| 126 |
|
| 127 |
end MetalNonMetalInteractions |
| 128 |
|
| 129 |
|
| 130 |
begin ChargeAtomTypes |
| 131 |
// Name charge |
| 132 |
O_TIP3P -0.834 |
| 133 |
O_SPCE -0.8476 |
| 134 |
O_SPC -0.82 |
| 135 |
H_TIP3P 0.417 |
| 136 |
H_TIP4P 0.520 |
| 137 |
H_TIP4P-Ew 0.52422 |
| 138 |
H_TIP5P 0.241 |
| 139 |
H_SPCE 0.4238 |
| 140 |
H_SPC 0.42 |
| 141 |
EP_TIP4P -1.040 |
| 142 |
EP_TIP4P-Ew -1.04844 |
| 143 |
EP_TIP5P -0.241 |
| 144 |
end ChargeAtomTypes |
| 145 |
|
| 146 |
begin MultipoleAtomTypes |
| 147 |
// OOPSE currently only supports charge-charge, charge-dipole, |
| 148 |
// dipole-dipole, and charge-quadrupole interactions. |
| 149 |
// Dipoles may be either traditional point-dipoles or split-dipoles. |
| 150 |
// possible formats for a multipolar atom type are: |
| 151 |
// |
| 152 |
// Point-dipoles: |
| 153 |
// name d phi theta psi dipole_moment |
| 154 |
// |
| 155 |
// Split-dipoles: |
| 156 |
// name s phi theta psi dipole_moment splitdipole_distance |
| 157 |
// |
| 158 |
// Point-Quadrupoles: |
| 159 |
// name q phi theta psi Qxx Qyy Qzz |
| 160 |
// |
| 161 |
// Atoms with both dipole and quadrupole moments: |
| 162 |
// name dq phi theta psi dipole_moment Qxx Qyy Qzz |
| 163 |
// |
| 164 |
// Atoms with both split dipoles and quadrupole moments: |
| 165 |
// name sq phi theta psi dipole_moment splitdipole_distance Qxx Qyy Qzz |
| 166 |
// |
| 167 |
// Euler angles are given in zxz convention in units of degrees. |
| 168 |
// |
| 169 |
// Charges are given in units of electrons. |
| 170 |
// |
| 171 |
// Dipoles are given in units of Debyes. |
| 172 |
// |
| 173 |
// Split dipole distances are given in units of Angstroms. |
| 174 |
// |
| 175 |
// Quadrupole moments are given in units of 10^-26 esu cm^2 (also known as an |
| 176 |
// esu centi-barn) |
| 177 |
// |
| 178 |
SSD_E dq 0.0 0.0 0.0 2.42 -1.682 1.762 -0.08 |
| 179 |
SSD_RF dq 0.0 0.0 0.0 2.48 -1.682 1.762 -0.08 |
| 180 |
SSD dq 0.0 0.0 0.0 2.35 -1.682 1.762 -0.08 |
| 181 |
SSD1 dq 0.0 0.0 0.0 2.35 -1.682 1.762 -0.08 |
| 182 |
end MultipoleAtomTypes |
| 183 |
|
| 184 |
begin StickyAtomTypes |
| 185 |
//name w0 v0 (kcal/mol) v0p rl (Ang) ru rlp rup |
| 186 |
SSD_E 0.07715 3.90 3.90 2.40 3.80 2.75 3.35 |
| 187 |
SSD_RF 0.07715 3.90 3.90 2.40 3.80 2.75 3.35 |
| 188 |
SSD 0.07715 3.7284 3.7284 2.75 3.35 2.75 4.0 |
| 189 |
SSD1 0.07715 3.6613 3.6613 2.75 3.35 2.75 4.0 |
| 190 |
end StickyAtomTypes |
| 191 |
|
| 192 |
|
| 193 |
begin BondTypes |
| 194 |
|
| 195 |
//Atom1 Atom2 Fixed |
| 196 |
//V_Fixed = 0 |
| 197 |
|
| 198 |
//Atom1 Atom2 Harmonic b0 Kb (kcal/mol) |
| 199 |
//V_Harmonic = 0.5*Kb(b- bo)^2 |
| 200 |
//Harmonic Examples |
| 201 |
CH3 CH3 Harmonic 1.526 260 |
| 202 |
CH3 CH2 Harmonic 1.526 260 |
| 203 |
CH3 CH Harmonic 1.526 260 |
| 204 |
CH2 CH2 Harmonic 1.526 260 |
| 205 |
CH2 CH Harmonic 1.526 260 |
| 206 |
CH CH Harmonic 1.526 260 |
| 207 |
S CH2 Harmonic 1.82 260 |
| 208 |
|
| 209 |
//Atom1 Atom2 Cubic b0 K3 K2 K1 K0 |
| 210 |
//V_Cubic = K3(b - b0)^3 + K2(b - b0)^2 + K1(b - b0) + K0 |
| 211 |
|
| 212 |
|
| 213 |
//Atom1 Atom2 Quartic b0 K4 K3 K2 K1 K0 |
| 214 |
//V_Quartic = K4(b - b0)^4 + K3(b - b0)^3 + K2(b - b0)^2 + K1(b - b0) + K0 |
| 215 |
|
| 216 |
|
| 217 |
//Atom1 Atom2 Polynomial b0 i Ki [j Kj] |
| 218 |
//V_Quartic = Ki(b - b0)^i + Kj(b - b0)^j + ... |
| 219 |
|
| 220 |
|
| 221 |
end BondTypes |
| 222 |
|
| 223 |
begin BendTypes |
| 224 |
|
| 225 |
//Harmonic |
| 226 |
//Atom1 Atom2 Atom3 Harmonic Theta0 Ktheta |
| 227 |
//V_Harmonic = 0.5*Ktheta(Theta - Theta0)^2 |
| 228 |
//Ktheta: kcal/mole/rad**2 |
| 229 |
//Theta0: degrees |
| 230 |
//Harmonic examples |
| 231 |
// |
| 232 |
CH3 CH2 CH3 Harmonic 114.0 117.68 |
| 233 |
CH3 CH2 CH2 Harmonic 114.0 117.68 |
| 234 |
CH3 CH2 CH Harmonic 114.0 117.68 |
| 235 |
CH3 CH CH3 Harmonic 112.0 117.68 |
| 236 |
CH3 CH CH2 Harmonic 112.0 117.68 |
| 237 |
CH3 CH CH Harmonic 112.0 117.68 |
| 238 |
CH2 CH2 CH2 Harmonic 114.0 117.68 |
| 239 |
CH2 CH2 CH Harmonic 114.0 117.68 |
| 240 |
CH2 CH CH2 Harmonic 112.0 117.68 |
| 241 |
CH2 CH CH Harmonic 112.0 117.68 |
| 242 |
CH CH2 CH Harmonic 114.0 117.68 |
| 243 |
CH CH CH Harmonic 112.0 117.68 |
| 244 |
S CH2 CH2 Harmonic 114.0 117.68 |
| 245 |
|
| 246 |
|
| 247 |
//UreyBradley |
| 248 |
//Atom1 Atom2 Atom3 UreyBradley Theta0 Ktheta S0 Kub |
| 249 |
//V_UreyBradleyBend = Ktheta(Theta - Theta0)^2 + Kub(S - S0)^2 |
| 250 |
//Ktheta: kcal/mole/rad**2 |
| 251 |
//Theta0: degrees |
| 252 |
//Kub: kcal/mole/A**2 |
| 253 |
//S0: A |
| 254 |
|
| 255 |
//Cubic |
| 256 |
//Atom1 Atom2 Atom3 Cubic Theta0 K3 K2 K1 K0 |
| 257 |
//V_Cubic = K3(Theta - Theta0)^3 + K2(Theta - Theta0)^2 + K1(Theta - Theta0) + K0 |
| 258 |
|
| 259 |
//Quartic |
| 260 |
//Atom1 Atom2 Atom3 Quartic Theta0 K4 K3 K2 K1 K0 |
| 261 |
//V_Quartic = K4(Theta - Theta0)^4 + K3(Theta - Theta0)^3 + K2(Theta - Theta0)^2 + K1(Theta - Theta0) + K0 |
| 262 |
|
| 263 |
//Polynomial |
| 264 |
//Atom1 Atom2 Atom3 Polynomial Theta0 i Ki [j Kj] |
| 265 |
//V_Polynomial = Ki(Theta - Theta0)^i + Kj(Theta - Theta0)^j + ... |
| 266 |
|
| 267 |
end BendTypes |
| 268 |
|
| 269 |
begin TorsionTypes |
| 270 |
|
| 271 |
//Cubic |
| 272 |
//Atom1 Atom2 Atom3 Atom4 Cubic k3 k2 k1 k0 ( all are kcal/mol ) |
| 273 |
//V_Cubic = k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0 |
| 274 |
//Cubic Examples |
| 275 |
CH3 CH2 CH2 CH3 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 276 |
CH3 CH2 CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 277 |
CH3 CH CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 278 |
CH3 CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 279 |
CH3 CH2 CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 280 |
CH3 CH CH2 CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 281 |
CH3 CH CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 282 |
CH3 CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 283 |
CH3 CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 284 |
CH3 CH CH2 CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 285 |
CH3 CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 286 |
CH2 CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 287 |
CH2 CH2 CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 288 |
CH2 CH CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 289 |
CH2 CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 290 |
CH2 CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 291 |
CH2 CH CH2 CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 292 |
CH2 CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 293 |
CH CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 294 |
CH CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 295 |
CH CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 296 |
S CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 297 |
|
| 298 |
//Charmm |
| 299 |
//Atom1 Atom2 Atom3 Atom4 Charmm Kchi n delta [Kchi n delta] |
| 300 |
//V_Charmm = Kchi(1 + cos(n(chi) - delta)) |
| 301 |
//Kchi: kcal/mole |
| 302 |
//n: multiplicity |
| 303 |
//delta: degrees |
| 304 |
//in some cases, a Charmm may have two or three terms. If n is equal to 0, it falls back to harmonic form |
| 305 |
|
| 306 |
//Quartic |
| 307 |
//Atom1 Atom2 Atom3 Atom4 Quartic k4 k3 k2 k1 k0 ( all are kcal/mol ) |
| 308 |
//V_Quartic = k4(cos phi)^4 + k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0 |
| 309 |
|
| 310 |
//Polynomial |
| 311 |
//Atom1 Atom2 Atom3 Atom4 Polynomial i Ki [j Kj] |
| 312 |
//VPolynomial = Ki (cos phi)^i + ... + Kj (cos phi)^j |
| 313 |
|
| 314 |
end TorsionTypes |
| 315 |
|
| 316 |
|
