| 1 |
chuckv |
1154 |
// 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 |
chuckv |
1257 |
|
| 13 |
gezelter |
1279 |
begin BaseAtomTypes |
| 14 |
chuckv |
1154 |
//Name mass (amu) |
| 15 |
|
|
CH4 16.05 |
| 16 |
|
|
CH3 15.04 |
| 17 |
|
|
CH2 14.03 |
| 18 |
chuckv |
1250 |
CH 13.02 |
| 19 |
chuckv |
1276 |
// Aromatic CH as in benzene |
| 20 |
|
|
CHar 13.02 |
| 21 |
|
|
// |
| 22 |
|
|
RCHar 12.0107 |
| 23 |
chuckv |
1257 |
// CH3 (sp3) thiol/sulfide/disulfide |
| 24 |
|
|
CH3S 15.04 |
| 25 |
|
|
// CH2 (sp3) thiol/sulfide/disulfide |
| 26 |
|
|
CH2S 14.03 |
| 27 |
|
|
//CH (sp3) all other/thiol |
| 28 |
|
|
CHS 13.02 |
| 29 |
|
|
//C (sp3) all other/thiol |
| 30 |
|
|
CS 12.0107 |
| 31 |
|
|
// sulfone |
| 32 |
|
|
SYZ 32.0655 |
| 33 |
|
|
// O in sulfone |
| 34 |
chuckv |
1259 |
//OY |
| 35 |
chuckv |
1257 |
// thiol S |
| 36 |
|
|
SH 32.0655 |
| 37 |
|
|
//Thiol H |
| 38 |
|
|
HS 1.0079 |
| 39 |
chuckv |
1259 |
//Thiol S |
| 40 |
|
|
S 32.0655 |
| 41 |
chuckv |
1257 |
// Sulfoxide |
| 42 |
|
|
SZ 32.0655 |
| 43 |
|
|
// Sulfur in disulfide |
| 44 |
|
|
SS 32.0655 |
| 45 |
|
|
// Sulfur in aromatic (thiophene) |
| 46 |
|
|
SP 32.0655 |
| 47 |
|
|
// sp2 carbon in thiophene |
| 48 |
|
|
CS 12.0107 |
| 49 |
|
|
// Sulfur attached to gold |
| 50 |
|
|
SAu 228.9807 |
| 51 |
|
|
|
| 52 |
chuckv |
1276 |
|
| 53 |
chuckv |
1257 |
//Water |
| 54 |
chuckv |
1154 |
SSD 18.0153 |
| 55 |
|
|
SSD1 18.0153 |
| 56 |
|
|
SSD_E 18.0153 |
| 57 |
|
|
SSD_RF 18.0153 |
| 58 |
|
|
O_TIP3P 15.9994 |
| 59 |
|
|
O_TIP4P 15.9994 |
| 60 |
|
|
O_TIP4P-Ew 15.9994 |
| 61 |
|
|
O_TIP5P 15.9994 |
| 62 |
|
|
O_TIP5P-E 15.9994 |
| 63 |
|
|
O_SPCE 15.9994 |
| 64 |
|
|
O_SPC 15.9994 |
| 65 |
|
|
H_TIP3P 1.0079 |
| 66 |
|
|
H_TIP4P 1.0079 |
| 67 |
|
|
H_TIP4P-Ew 1.0079 |
| 68 |
|
|
H_TIP5P 1.0079 |
| 69 |
|
|
H_SPCE 1.0079 |
| 70 |
|
|
H_SPC 1.0079 |
| 71 |
|
|
EP_TIP4P 0.0 |
| 72 |
|
|
EP_TIP4P-Ew 0.0 |
| 73 |
|
|
EP_TIP5P 0.0 |
| 74 |
chuckv |
1257 |
|
| 75 |
|
|
//Standard Atoms |
| 76 |
chuckv |
1154 |
C 12.0107 |
| 77 |
|
|
S 32.0655 |
| 78 |
|
|
Ni 58.710 |
| 79 |
|
|
Cu 63.550 |
| 80 |
|
|
Rh 102.90550 |
| 81 |
|
|
Pd 106.42 |
| 82 |
|
|
Ag 107.8682 |
| 83 |
|
|
Ir 192.217 |
| 84 |
|
|
Pt 195.09 |
| 85 |
|
|
Au 196.97 |
| 86 |
gezelter |
1279 |
end BaseAtomTypes |
| 87 |
|
|
|
| 88 |
|
|
begin AtomTypes |
| 89 |
chuckv |
1154 |
end AtomTypes |
| 90 |
|
|
|
| 91 |
|
|
begin DirectionalAtomTypes |
| 92 |
|
|
//Name I_xx I_yy I_zz (All moments in (amu*Ang^2) |
| 93 |
gezelter |
1775 |
//Au 0.24437807 0.24437807 0.00 |
| 94 |
chuckv |
1154 |
SSD 1.7696 0.6145 1.1550 |
| 95 |
|
|
SSD1 1.7696 0.6145 1.1550 |
| 96 |
|
|
SSD_E 1.7696 0.6145 1.1550 |
| 97 |
|
|
SSD_RF 1.7696 0.6145 1.1550 |
| 98 |
|
|
end DirectionalAtomTypes |
| 99 |
|
|
|
| 100 |
|
|
|
| 101 |
|
|
begin LennardJonesAtomTypes |
| 102 |
|
|
//Name epsilon sigma |
| 103 |
|
|
SSD 0.152 3.051 |
| 104 |
|
|
SSD1 0.152 3.016 |
| 105 |
|
|
SSD_E 0.152 3.035 |
| 106 |
|
|
SSD_RF 0.152 3.019 |
| 107 |
|
|
O_TIP3P 0.1521 3.15061 |
| 108 |
|
|
O_TIP4P 0.1550 3.15365 |
| 109 |
|
|
O_TIP4P-Ew 0.16275 3.16435 |
| 110 |
|
|
O_TIP5P 0.16 3.12 |
| 111 |
|
|
O_TIP5P-E 0.178 3.097 |
| 112 |
|
|
O_SPCE 0.15532 3.16549 |
| 113 |
|
|
O_SPC 0.15532 3.16549 |
| 114 |
chuckv |
1257 |
// From TraPPE-UA JPCB, 109, 24100 and JCPB 102,2569 |
| 115 |
|
|
CH4 0.2941 3.73 |
| 116 |
|
|
CH3 0.1947 3.75 |
| 117 |
|
|
CH2 0.09140 3.95 |
| 118 |
|
|
CH 0.0987 4.68 |
| 119 |
|
|
CS 0.0009935 6.40 |
| 120 |
|
|
CH3S 0.1947 3.75 |
| 121 |
|
|
CH2S 0.09140 3.95 |
| 122 |
|
|
CHS 0.0987 4.68 |
| 123 |
chuckv |
1276 |
// From CPC 177 2007 S-S distance on gold surfaces is 4.45 |
| 124 |
|
|
S 0.3954 4.45 |
| 125 |
chuckv |
1257 |
SH 0.4610 3.62 |
| 126 |
|
|
SS 0.3279 3.72 |
| 127 |
|
|
SP 0.3576 3.60 |
| 128 |
chuckv |
1276 |
//From TraPPE-UA JPCB 104, 8008 |
| 129 |
|
|
CHar 0.1003 3.695 |
| 130 |
|
|
RCHar 0.04173 3.88 |
| 131 |
chuckv |
1259 |
// ---- End From TraPPE-UA |
| 132 |
chuckv |
1276 |
|
| 133 |
chuckv |
1154 |
end LennardJonesAtomTypes |
| 134 |
|
|
|
| 135 |
chuckv |
1159 |
begin SCAtomTypes |
| 136 |
|
|
// Name epsilon(eV) c m n alpha(angstroms) |
| 137 |
|
|
Ni 0.0073767 84.745 5.0 10.0 3.5157 |
| 138 |
|
|
Cu 0.0057921 84.843 5.0 10.0 3.6030 |
| 139 |
|
|
Rh 0.0024612 305.499 5.0 13.0 3.7984 |
| 140 |
|
|
Pd 0.0032864 148.205 6.0 12.0 3.8813 |
| 141 |
|
|
Ag 0.0039450 96.524 6.0 11.0 4.0691 |
| 142 |
|
|
Ir 0.0037674 224.815 6.0 13.0 3.8344 |
| 143 |
|
|
Pt 0.0097894 71.336 7.0 11.0 3.9163 |
| 144 |
|
|
Au 0.0078052 53.581 8.0 11.0 4.0651 |
| 145 |
|
|
end SCAtomTypes |
| 146 |
|
|
|
| 147 |
|
|
|
| 148 |
|
|
// Metal non-metal interactions. |
| 149 |
gezelter |
1544 |
// Format: Metal Atom, Non-Metal Atom, Interaction Type, Interaction Parameters |
| 150 |
|
|
// Interaction type can be: MAW, LennardJones or ShiftedMorse or RepulsiveMorse |
| 151 |
|
|
begin NonBondedInteractions |
| 152 |
chuckv |
1159 |
|
| 153 |
|
|
//MAW (Metal Angular Water section) |
| 154 |
chuckv |
1242 |
// r_e, D_e beta ca1 cb1 |
| 155 |
|
|
Cu SSD_E MAW 2.5525 1.9850 1.1680 1.1250 0.750000 |
| 156 |
chuckv |
1245 |
Au SSD_E MAW 2.68 0.6 1.33 0.95 -0.25 |
| 157 |
chuckv |
1159 |
|
| 158 |
|
|
//LennardJones |
| 159 |
|
|
// sigma epsilon |
| 160 |
chuckv |
1254 |
Au CH3 LennardJones 3.54 0.2146 |
| 161 |
|
|
Au CH2 LennardJones 3.54 0.1749 |
| 162 |
chuckv |
1276 |
//Au SH LennardJones 2.40 8.465 |
| 163 |
|
|
Au S LennardJones 2.40 8.465 |
| 164 |
chuckv |
1159 |
|
| 165 |
|
|
//Shifted Morse |
| 166 |
|
|
// r0 D0 beta0 |
| 167 |
chuckv |
1229 |
Au O_SPCE ShiftedMorse 3.70 0.0424 0.769 |
| 168 |
chuckv |
1159 |
|
| 169 |
|
|
//Repulsive Morse |
| 170 |
|
|
// r0 D0 beta0 |
| 171 |
chuckv |
1229 |
Au H_SPCE RepulsiveMorse -1.00 0.00850 0.769 |
| 172 |
gezelter |
1625 |
|
| 173 |
|
|
//Repulsive Power |
| 174 |
|
|
Au ON RepulsivePower 3.47005 0.186208 11 |
| 175 |
|
|
Au NO RepulsivePower 3.53955 0.168629 11 |
| 176 |
gezelter |
1544 |
end NonBondedInteractions |
| 177 |
chuckv |
1159 |
|
| 178 |
|
|
|
| 179 |
chuckv |
1154 |
begin ChargeAtomTypes |
| 180 |
|
|
// Name charge |
| 181 |
|
|
O_TIP3P -0.834 |
| 182 |
|
|
O_SPCE -0.8476 |
| 183 |
|
|
O_SPC -0.82 |
| 184 |
|
|
H_TIP3P 0.417 |
| 185 |
|
|
H_TIP4P 0.520 |
| 186 |
|
|
H_TIP4P-Ew 0.52422 |
| 187 |
|
|
H_TIP5P 0.241 |
| 188 |
|
|
H_SPCE 0.4238 |
| 189 |
|
|
H_SPC 0.42 |
| 190 |
|
|
EP_TIP4P -1.040 |
| 191 |
|
|
EP_TIP4P-Ew -1.04844 |
| 192 |
|
|
EP_TIP5P -0.241 |
| 193 |
|
|
end ChargeAtomTypes |
| 194 |
|
|
|
| 195 |
|
|
begin MultipoleAtomTypes |
| 196 |
gezelter |
1390 |
// OpenMD currently only supports charge-charge, charge-dipole, |
| 197 |
chuckv |
1154 |
// dipole-dipole, and charge-quadrupole interactions. |
| 198 |
|
|
// Dipoles may be either traditional point-dipoles or split-dipoles. |
| 199 |
|
|
// possible formats for a multipolar atom type are: |
| 200 |
|
|
// |
| 201 |
|
|
// Point-dipoles: |
| 202 |
|
|
// name d phi theta psi dipole_moment |
| 203 |
|
|
// |
| 204 |
|
|
// Split-dipoles: |
| 205 |
|
|
// name s phi theta psi dipole_moment splitdipole_distance |
| 206 |
|
|
// |
| 207 |
|
|
// Point-Quadrupoles: |
| 208 |
|
|
// name q phi theta psi Qxx Qyy Qzz |
| 209 |
|
|
// |
| 210 |
|
|
// Atoms with both dipole and quadrupole moments: |
| 211 |
|
|
// name dq phi theta psi dipole_moment Qxx Qyy Qzz |
| 212 |
|
|
// |
| 213 |
|
|
// Atoms with both split dipoles and quadrupole moments: |
| 214 |
|
|
// name sq phi theta psi dipole_moment splitdipole_distance Qxx Qyy Qzz |
| 215 |
|
|
// |
| 216 |
|
|
// Euler angles are given in zxz convention in units of degrees. |
| 217 |
|
|
// |
| 218 |
|
|
// Charges are given in units of electrons. |
| 219 |
|
|
// |
| 220 |
|
|
// Dipoles are given in units of Debyes. |
| 221 |
|
|
// |
| 222 |
|
|
// Split dipole distances are given in units of Angstroms. |
| 223 |
|
|
// |
| 224 |
|
|
// Quadrupole moments are given in units of 10^-26 esu cm^2 (also known as an |
| 225 |
|
|
// esu centi-barn) |
| 226 |
|
|
// |
| 227 |
|
|
SSD_E dq 0.0 0.0 0.0 2.42 -1.682 1.762 -0.08 |
| 228 |
|
|
SSD_RF dq 0.0 0.0 0.0 2.48 -1.682 1.762 -0.08 |
| 229 |
|
|
SSD dq 0.0 0.0 0.0 2.35 -1.682 1.762 -0.08 |
| 230 |
|
|
SSD1 dq 0.0 0.0 0.0 2.35 -1.682 1.762 -0.08 |
| 231 |
|
|
end MultipoleAtomTypes |
| 232 |
|
|
|
| 233 |
|
|
begin StickyAtomTypes |
| 234 |
|
|
//name w0 v0 (kcal/mol) v0p rl (Ang) ru rlp rup |
| 235 |
|
|
SSD_E 0.07715 3.90 3.90 2.40 3.80 2.75 3.35 |
| 236 |
|
|
SSD_RF 0.07715 3.90 3.90 2.40 3.80 2.75 3.35 |
| 237 |
|
|
SSD 0.07715 3.7284 3.7284 2.75 3.35 2.75 4.0 |
| 238 |
|
|
SSD1 0.07715 3.6613 3.6613 2.75 3.35 2.75 4.0 |
| 239 |
|
|
end StickyAtomTypes |
| 240 |
|
|
|
| 241 |
|
|
|
| 242 |
|
|
begin BondTypes |
| 243 |
|
|
|
| 244 |
|
|
//Atom1 Atom2 Fixed |
| 245 |
|
|
//V_Fixed = 0 |
| 246 |
|
|
|
| 247 |
|
|
//Atom1 Atom2 Harmonic b0 Kb (kcal/mol) |
| 248 |
|
|
//V_Harmonic = 0.5*Kb(b- bo)^2 |
| 249 |
|
|
//Harmonic Examples |
| 250 |
|
|
CH3 CH3 Harmonic 1.526 260 |
| 251 |
|
|
CH3 CH2 Harmonic 1.526 260 |
| 252 |
|
|
CH3 CH Harmonic 1.526 260 |
| 253 |
|
|
CH2 CH2 Harmonic 1.526 260 |
| 254 |
|
|
CH2 CH Harmonic 1.526 260 |
| 255 |
|
|
CH CH Harmonic 1.526 260 |
| 256 |
kfletche |
1256 |
// fix the Kb for the thiol below: |
| 257 |
chuckv |
1259 |
S CH2 Harmonic 1.82 281 |
| 258 |
|
|
SH CH2 Harmonic 1.82 281 |
| 259 |
chuckv |
1154 |
|
| 260 |
|
|
//Atom1 Atom2 Cubic b0 K3 K2 K1 K0 |
| 261 |
|
|
//V_Cubic = K3(b - b0)^3 + K2(b - b0)^2 + K1(b - b0) + K0 |
| 262 |
|
|
|
| 263 |
|
|
|
| 264 |
|
|
//Atom1 Atom2 Quartic b0 K4 K3 K2 K1 K0 |
| 265 |
|
|
//V_Quartic = K4(b - b0)^4 + K3(b - b0)^3 + K2(b - b0)^2 + K1(b - b0) + K0 |
| 266 |
|
|
|
| 267 |
|
|
|
| 268 |
|
|
//Atom1 Atom2 Polynomial b0 i Ki [j Kj] |
| 269 |
|
|
//V_Quartic = Ki(b - b0)^i + Kj(b - b0)^j + ... |
| 270 |
|
|
|
| 271 |
|
|
|
| 272 |
|
|
end BondTypes |
| 273 |
|
|
|
| 274 |
|
|
begin BendTypes |
| 275 |
|
|
|
| 276 |
|
|
//Harmonic |
| 277 |
|
|
//Atom1 Atom2 Atom3 Harmonic Theta0 Ktheta |
| 278 |
|
|
//V_Harmonic = 0.5*Ktheta(Theta - Theta0)^2 |
| 279 |
|
|
//Ktheta: kcal/mole/rad**2 |
| 280 |
|
|
//Theta0: degrees |
| 281 |
|
|
//Harmonic examples |
| 282 |
|
|
// |
| 283 |
chuckv |
1259 |
//CH3 CH2 CH3 Harmonic 114.0 117.68 |
| 284 |
|
|
//CH3 CH2 CH2 Harmonic 114.0 117.68 |
| 285 |
|
|
//CH3 CH2 CH Harmonic 114.0 117.68 |
| 286 |
|
|
//CH3 CH CH3 Harmonic 112.0 117.68 |
| 287 |
|
|
//CH3 CH CH2 Harmonic 112.0 117.68 |
| 288 |
|
|
//CH3 CH CH Harmonic 112.0 117.68 |
| 289 |
|
|
//CH2 CH2 CH2 Harmonic 114.0 117.68 |
| 290 |
|
|
//CH2 CH2 CH Harmonic 114.0 117.68 |
| 291 |
chuckv |
1154 |
CH2 CH CH2 Harmonic 112.0 117.68 |
| 292 |
|
|
CH2 CH CH Harmonic 112.0 117.68 |
| 293 |
chuckv |
1259 |
//CH CH2 CH Harmonic 114.0 117.68 |
| 294 |
chuckv |
1154 |
CH CH CH Harmonic 112.0 117.68 |
| 295 |
|
|
|
| 296 |
chuckv |
1259 |
//From Lubna et al.JPCB 109, 24100 (2005) TraPPE |
| 297 |
|
|
CH3 CH2 SH Harmonic 96.0 67.220 |
| 298 |
|
|
CH2 CH2 SH Harmonic 96.0 67.220 |
| 299 |
|
|
CH2 CH2 S Harmonic 114.0 124.19 |
| 300 |
|
|
CH3 CH2 S Harmonic 114.0 124.19 |
| 301 |
|
|
CH3 CH2 CH3 Harmonic 114.0 124.19 |
| 302 |
|
|
CH3 CH2 CH2 Harmonic 114.0 124.19 |
| 303 |
|
|
CH2 CH2 CH2 Harmonic 114.0 124.19 |
| 304 |
|
|
CH3 CH2 CH Harmonic 114.0 124.19 |
| 305 |
chuckv |
1154 |
|
| 306 |
chuckv |
1259 |
|
| 307 |
chuckv |
1154 |
//UreyBradley |
| 308 |
|
|
//Atom1 Atom2 Atom3 UreyBradley Theta0 Ktheta S0 Kub |
| 309 |
|
|
//V_UreyBradleyBend = Ktheta(Theta - Theta0)^2 + Kub(S - S0)^2 |
| 310 |
|
|
//Ktheta: kcal/mole/rad**2 |
| 311 |
|
|
//Theta0: degrees |
| 312 |
|
|
//Kub: kcal/mole/A**2 |
| 313 |
|
|
//S0: A |
| 314 |
|
|
|
| 315 |
|
|
//Cubic |
| 316 |
|
|
//Atom1 Atom2 Atom3 Cubic Theta0 K3 K2 K1 K0 |
| 317 |
|
|
//V_Cubic = K3(Theta - Theta0)^3 + K2(Theta - Theta0)^2 + K1(Theta - Theta0) + K0 |
| 318 |
|
|
|
| 319 |
|
|
//Quartic |
| 320 |
|
|
//Atom1 Atom2 Atom3 Quartic Theta0 K4 K3 K2 K1 K0 |
| 321 |
|
|
//V_Quartic = K4(Theta - Theta0)^4 + K3(Theta - Theta0)^3 + K2(Theta - Theta0)^2 + K1(Theta - Theta0) + K0 |
| 322 |
|
|
|
| 323 |
|
|
//Polynomial |
| 324 |
|
|
//Atom1 Atom2 Atom3 Polynomial Theta0 i Ki [j Kj] |
| 325 |
|
|
//V_Polynomial = Ki(Theta - Theta0)^i + Kj(Theta - Theta0)^j + ... |
| 326 |
|
|
|
| 327 |
|
|
end BendTypes |
| 328 |
|
|
|
| 329 |
|
|
begin TorsionTypes |
| 330 |
|
|
|
| 331 |
kfletche |
1256 |
// All thiol torsions from Kautman and Klein (J. Phys. Chem. 1989, 91, 4994-5001) |
| 332 |
|
|
|
| 333 |
chuckv |
1257 |
//S CH2 CH2 CH3 Polynomial 0 2.218 1 2.905 2 -3.136 3 -0.7313 4 6.272 5 -7.528 |
| 334 |
|
|
//S CH2 CH2 CH2 Polynomial 0 2.218 1 2.905 2 -3.136 3 -0.7313 4 6.272 5 -7.528 |
| 335 |
|
|
//S CH2 CH2 CH Polynomial 0 2.218 1 2.905 2 -3.136 3 -0.7313 4 6.272 5 -7.528 |
| 336 |
|
|
//S CH2 CH2 C Polynomial 0 2.218 1 2.905 2 -3.136 3 -0.7313 4 6.272 5 -7.528 |
| 337 |
kfletche |
1256 |
|
| 338 |
|
|
// All type 1 possibilities from Dubbeldam et al. (J. Phys. Chem. B 2004, 108, 12301-12313) |
| 339 |
|
|
|
| 340 |
chuckv |
1257 |
//CH3 CH2 CH2 CH3 Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
| 341 |
|
|
//CH3 CH2 CH2 CH2 Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
| 342 |
|
|
//CH3 CH2 CH2 CH Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
| 343 |
|
|
//CH3 CH2 CH2 C Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
| 344 |
|
|
//CH2 CH2 CH2 CH2 Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
| 345 |
|
|
//CH2 CH2 CH2 CH Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
| 346 |
|
|
//CH2 CH2 CH2 C Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
| 347 |
|
|
//CH CH2 CH2 CH Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
| 348 |
|
|
//CH CH2 CH2 C Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
| 349 |
|
|
//C CH2 CH2 C Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
| 350 |
kfletche |
1256 |
|
| 351 |
|
|
// All type 2 possibilities: |
| 352 |
|
|
|
| 353 |
chuckv |
1257 |
//H CH CH2 CH3 Polynomial 0 2.7167 1 8.665 2 0.82669 3 -12.92 4 -1.653 5 3.2712 |
| 354 |
|
|
//H CH CH2 CH2 Polynomial 0 2.7161 1 8.665 2 0.82669 3 -12.92 4 -1.653 5 3.2712 |
| 355 |
|
|
//H CH CH2 CH Polynomial 0 2.7161 1 8.665 2 0.82669 3 -12.92 4 -1.653 5 3.2712 |
| 356 |
|
|
//H CH CH2 C Polynomial 0 2.7161 1 8.665 2 0.82669 3 -12.92 4 -1.653 5 3.2712 |
| 357 |
kfletche |
1256 |
|
| 358 |
|
|
// All type 3 possibilities: |
| 359 |
|
|
|
| 360 |
chuckv |
1257 |
//CH3 C CH2 CH3 Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
| 361 |
|
|
//CH3 C CH2 CH2 Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
| 362 |
|
|
//CH3 C CH2 CH Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
| 363 |
|
|
//CH3 C CH2 C Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
| 364 |
|
|
//CH2 C CH2 CH2 Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
| 365 |
|
|
//CH2 C CH2 CH Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
| 366 |
|
|
//CH2 C CH2 C Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
| 367 |
|
|
//CH C CH2 CH Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
| 368 |
|
|
//CH C CH2 C Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
| 369 |
|
|
//C C CH2 C Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
| 370 |
kfletche |
1256 |
|
| 371 |
|
|
// All type 4 possibilities: |
| 372 |
|
|
|
| 373 |
chuckv |
1257 |
//CH3 C C CH3 Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
| 374 |
|
|
//CH3 C C CH2 Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
| 375 |
|
|
//CH3 C C CH Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
| 376 |
|
|
//CH3 C C C Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
| 377 |
|
|
//CH2 C C CH2 Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
| 378 |
|
|
//CH2 C C CH Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
| 379 |
|
|
//CH2 C C C Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
| 380 |
|
|
//CH C C CH Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
| 381 |
|
|
//CH C C C Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
| 382 |
|
|
//C C C C Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
| 383 |
kfletche |
1256 |
|
| 384 |
|
|
//All type 5 possibilities: |
| 385 |
|
|
|
| 386 |
chuckv |
1257 |
//CH3 C CH H Polynomial 0 3.1301 1 9.390 2 0 3 -12.52 4 0 5 0 |
| 387 |
|
|
//CH2 C CH H Polynomial 0 3.1301 1 9.390 2 0 3 -12.52 4 0 5 0 |
| 388 |
|
|
//CH C CH H Polynomial 0 3.1301 1 9.390 2 0 3 -12.52 4 0 5 0 |
| 389 |
|
|
//C C CH H Polynomial 0 3.1301 1 9.390 2 0 3 -12.52 4 0 5 0 |
| 390 |
kfletche |
1256 |
|
| 391 |
|
|
//All type 6 possibilities: |
| 392 |
|
|
|
| 393 |
chuckv |
1257 |
//H CH CH H Polynomial 0 2.1706 1 5.609 2 -1.804 3 -5.976 4 3.6089 5 -3.6089 |
| 394 |
kfletche |
1256 |
|
| 395 |
chuckv |
1154 |
//Cubic |
| 396 |
|
|
//Atom1 Atom2 Atom3 Atom4 Cubic k3 k2 k1 k0 ( all are kcal/mol ) |
| 397 |
|
|
//V_Cubic = k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0 |
| 398 |
|
|
//Cubic Examples |
| 399 |
chuckv |
1259 |
//CH3 CH2 CH2 CH3 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 400 |
chuckv |
1257 |
CH3 CH2 CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 401 |
|
|
CH3 CH CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 402 |
chuckv |
1259 |
//CH3 CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 403 |
chuckv |
1257 |
CH3 CH2 CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 404 |
|
|
CH3 CH CH2 CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 405 |
|
|
CH3 CH CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 406 |
chuckv |
1259 |
//CH3 CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 407 |
chuckv |
1257 |
CH3 CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 408 |
|
|
CH3 CH CH2 CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 409 |
|
|
CH3 CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 410 |
chuckv |
1259 |
//CH2 CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 411 |
chuckv |
1257 |
CH2 CH2 CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 412 |
|
|
CH2 CH CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 413 |
|
|
CH2 CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 414 |
|
|
CH2 CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 415 |
|
|
CH2 CH CH2 CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 416 |
|
|
CH2 CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 417 |
|
|
CH CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 418 |
|
|
CH CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 419 |
|
|
CH CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 420 |
chuckv |
1259 |
//S CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 421 |
chuckv |
1154 |
|
| 422 |
chuckv |
1257 |
//Opls |
| 423 |
gezelter |
1258 |
//Atom1 Atom2 Atom3 Atom4 Opls v1 v2 v3 |
| 424 |
|
|
//V_Opls = v1 / 2 * [1 + cos(phi)] + v2 / 2 * [1 - cos(2*phi)] + v3 / 2 * [1 + cos(3*phi)] |
| 425 |
chuckv |
1257 |
//units for v_n: kcal / mol |
| 426 |
|
|
|
| 427 |
chuckv |
1259 |
|
| 428 |
gezelter |
1258 |
//Trappe |
| 429 |
|
|
//Atom1 Atom2 Atom3 Atom4 Trappe c0 c1 c2 c3 |
| 430 |
|
|
//V_Opls = c0 + c1 * [1 + cos(phi)] + c2 * [1 - cos(2*phi)] + c3 * [1 + cos(3*phi)] |
| 431 |
|
|
//units for c_n: kcal / mol |
| 432 |
chuckv |
1257 |
|
| 433 |
chuckv |
1259 |
//From Martin et al. JPCB 120, 2569 (1998) |
| 434 |
|
|
CH3 CH2 CH2 CH3 Trappe 0.0 0.70544 -0.13549 1.5723 |
| 435 |
|
|
CH3 CH2 CH2 CH2 Trappe 0.0 0.70544 -0.13549 1.5723 |
| 436 |
|
|
CH3 CH2 CH2 CH Trappe 0.0 0.70544 -0.13549 1.5723 |
| 437 |
|
|
CH2 CH2 CH2 CH2 Trappe 0.0 0.70544 -0.13549 1.5723 |
| 438 |
|
|
|
| 439 |
|
|
|
| 440 |
|
|
//From Lubna et al.JPCB 109, 24100 (2005) |
| 441 |
|
|
CH3 CH2 CH2 SH Trappe 0.10507 -0.10342 0.036680 0.60874 |
| 442 |
|
|
CH2 CH2 CH2 SH Trappe 0.10507 -0.10342 0.036680 0.60874 |
| 443 |
chuckv |
1273 |
// Thiol attached to a metal surface. |
| 444 |
|
|
CH3 CH2 CH2 S Trappe 0.10507 -0.10342 0.036680 0.60874 |
| 445 |
|
|
CH2 CH2 CH2 S Trappe 0.10507 -0.10342 0.036680 0.60874 |
| 446 |
chuckv |
1259 |
CH3 CH2 S CH2 Trappe 0.0 0.73041 -0.53685 1.1557 |
| 447 |
|
|
CH2 CH2 S CH2 Trappe 0.0 0.73041 -0.53685 1.1557 |
| 448 |
|
|
CH CH2 S CH2 Trappe 0.0 0.73041 -0.53685 1.1557 |
| 449 |
|
|
CH2 S S CH2 Trappe 3.5049 0.79083 -4.3348 1.003932 |
| 450 |
|
|
CH3 S S CH3 Trappe 3.5049 0.79083 -4.3348 1.003932 |
| 451 |
|
|
CH3 CH2 CH S Trappe -0.49886 0.85189 -0.22225 0.87680 |
| 452 |
|
|
CH3 CH2 CH S Trappe -0.49886 0.85189 -0.22225 0.87680 |
| 453 |
|
|
CH2 CH2 CH S Trappe -0.49886 0.85189 -0.22225 0.87680 |
| 454 |
|
|
CH CH2 CH S Trappe -0.49886 0.85189 -0.22225 0.87680 |
| 455 |
|
|
CH3 CH2 C S Trappe 0.0 0.0 0.0 0.91658 |
| 456 |
|
|
CH2 CH2 C S Trappe 0.0 0.0 0.0 0.91658 |
| 457 |
|
|
CH CH2 C S Trappe 0.0 0.0 0.0 0.91658 |
| 458 |
|
|
CH3 CG S H Trappe 0.0 0.0 0.0 0.79480 |
| 459 |
chuckv |
1276 |
//From TraPPE-UA JPCB 104, 8008 |
| 460 |
chuckv |
1259 |
|
| 461 |
chuckv |
1154 |
//Charmm |
| 462 |
|
|
//Atom1 Atom2 Atom3 Atom4 Charmm Kchi n delta [Kchi n delta] |
| 463 |
|
|
//V_Charmm = Kchi(1 + cos(n(chi) - delta)) |
| 464 |
|
|
//Kchi: kcal/mole |
| 465 |
|
|
//n: multiplicity |
| 466 |
|
|
//delta: degrees |
| 467 |
|
|
//in some cases, a Charmm may have two or three terms. If n is equal to 0, it falls back to harmonic form |
| 468 |
|
|
|
| 469 |
|
|
//Quartic |
| 470 |
|
|
//Atom1 Atom2 Atom3 Atom4 Quartic k4 k3 k2 k1 k0 ( all are kcal/mol ) |
| 471 |
|
|
//V_Quartic = k4(cos phi)^4 + k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0 |
| 472 |
|
|
|
| 473 |
|
|
//Polynomial |
| 474 |
|
|
//Atom1 Atom2 Atom3 Atom4 Polynomial i Ki [j Kj] |
| 475 |
|
|
//VPolynomial = Ki (cos phi)^i + ... + Kj (cos phi)^j |
| 476 |
|
|
|
| 477 |
chuckv |
1259 |
|
| 478 |
chuckv |
1154 |
end TorsionTypes |
| 479 |
|
|
|
| 480 |
|
|
|
