| 1 |
tim |
1921 |
// This is the forcefield file for the Dipolar Unified-atom Force Field (DUFF) |
| 2 |
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// |
| 3 |
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// The sections are divided into AtomTypes |
| 4 |
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// |
| 5 |
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//any parameters (but not all) are derived from the TRAPPE force field |
| 6 |
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// of Siepmann's group. |
| 7 |
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begin AtomTypes |
| 8 |
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//Name mass (amu) |
| 9 |
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CH4 16.05 |
| 10 |
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CH3 15.04 |
| 11 |
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CH2 14.03 |
| 12 |
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CH 13.02 |
| 13 |
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SSD 18.0153 |
| 14 |
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SSD1 18.0153 |
| 15 |
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SSD_E 18.0153 |
| 16 |
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SSD_RF 18.0153 |
| 17 |
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O_TIP3P 15.9994 |
| 18 |
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O_TIP4P 15.9994 |
| 19 |
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O_TIP5P 15.9994 |
| 20 |
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O_SPCE 15.9994 |
| 21 |
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O_SPC 15.9994 |
| 22 |
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H_TIP3P 1.0079 |
| 23 |
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H_TIP4P 1.0079 |
| 24 |
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H_TIP5P 1.0079 |
| 25 |
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H_SPCE 1.0079 |
| 26 |
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H_SPC 1.0079 |
| 27 |
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EP_TIP4P 0.0 |
| 28 |
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EP_TIP5P 0.0 |
| 29 |
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HEAD 196 |
| 30 |
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TB1 14.03 |
| 31 |
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TE1 15.04 |
| 32 |
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TB2 21.05 |
| 33 |
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TE2 22.56 |
| 34 |
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TB3 28.06 |
| 35 |
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TE3 30.08 |
| 36 |
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H 1.00794 |
| 37 |
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He 4.002602 |
| 38 |
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C 12.0107 |
| 39 |
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N 14.00674 |
| 40 |
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O 15.9994 |
| 41 |
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F 18.9984032 |
| 42 |
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Ne 20.1797 |
| 43 |
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S 32.066 |
| 44 |
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Cl 35.4527 |
| 45 |
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Ar 39.948 |
| 46 |
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Br 79.904 |
| 47 |
chrisfen |
2151 |
Kr 83.80 |
| 48 |
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Cl- 35.4527 |
| 49 |
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Na+ 22.9898 |
| 50 |
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Na 22.9898 |
| 51 |
tim |
1921 |
end AtomTypes |
| 52 |
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| 53 |
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begin DirectionalAtomTypes |
| 54 |
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//Name I_xx I_yy I_zz (All moments in (amu*Ang^2) |
| 55 |
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SSD 1.7696 0.6145 1.1550 |
| 56 |
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SSD1 1.7696 0.6145 1.1550 |
| 57 |
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SSD_E 1.7696 0.6145 1.1550 |
| 58 |
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SSD_RF 1.7696 0.6145 1.1550 |
| 59 |
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HEAD 1125 1125 250 |
| 60 |
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end DirectionalAtomTypes |
| 61 |
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| 62 |
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begin LennardJonesAtomTypes |
| 63 |
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//Name epsilon sigma |
| 64 |
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SSD 0.152 3.051 |
| 65 |
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SSD1 0.152 3.016 |
| 66 |
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SSD_E 0.152 3.035 |
| 67 |
chrisfen |
2130 |
SSD_RF 0.152 3.019 |
| 68 |
tim |
1921 |
O_TIP3P 0.1521 3.15061 |
| 69 |
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O_TIP4P 0.1550 3.15365 |
| 70 |
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O_TIP5P 0.16 3.12 |
| 71 |
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O_SPCE 0.15532 3.16549 |
| 72 |
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O_SPC 0.15532 3.16549 |
| 73 |
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CH4 0.279 3.73 |
| 74 |
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CH3 0.185 3.75 |
| 75 |
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CH2 0.0866 3.95 |
| 76 |
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CH 0.0189 4.68 |
| 77 |
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HEAD 0.185 .75 |
| 78 |
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TB1 0.0866 4.0 |
| 79 |
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TE1 0.185 4.0 |
| 80 |
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TB2 0.25 6.0 |
| 81 |
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TE2 0.5 6.0 |
| 82 |
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TB3 0.5 8.0 |
| 83 |
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TE3 0.75 8.0 |
| 84 |
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H 0.017090056482 2.81 |
| 85 |
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He 0.020269601874 2.28 |
| 86 |
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C 0.101745452544 3.35 |
| 87 |
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N 0.074123151951 3.31 |
| 88 |
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O 0.122412497592 2.95 |
| 89 |
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F 0.104924997936 2.83 |
| 90 |
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Ne 0.09339914589 2.72 |
| 91 |
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S 0.36366050421 3.52 |
| 92 |
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Cl 0.344781953445 3.35 |
| 93 |
|
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Ar 0.238068461226 3.41 |
| 94 |
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Br 0.511111921764 3.54 |
| 95 |
chrisfen |
2151 |
Kr 0.32590340268 3.83 |
| 96 |
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Cl- 0.1180 4.41724 |
| 97 |
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Na+ 0.002772 3.330445 |
| 98 |
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Na 0.002772 3.330445 |
| 99 |
tim |
1921 |
end LennardJonesAtomTypes |
| 100 |
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| 101 |
tim |
2096 |
begin ChargeAtomTypes |
| 102 |
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// Name charge |
| 103 |
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O_TIP3P -0.834 |
| 104 |
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O_SPCE -0.8476 |
| 105 |
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O_SPC -0.82 |
| 106 |
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H_TIP3P 0.417 |
| 107 |
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H_TIP4P 0.520 |
| 108 |
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H_TIP5P 0.241 |
| 109 |
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H_SPCE 0.4238 |
| 110 |
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H_SPC 0.42 |
| 111 |
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EP_TIP4P -1.040 |
| 112 |
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EP_TIP5P -0.241 |
| 113 |
chrisfen |
2151 |
Cl- -1.0 |
| 114 |
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Na+ 1.0 |
| 115 |
tim |
2096 |
end ChargeAtomTypes |
| 116 |
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| 117 |
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begin MultipoleAtomTypes |
| 118 |
gezelter |
2117 |
// OOPSE currently only supports charge-charge, charge-dipole, |
| 119 |
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// dipole-dipole, and charge-quadrupole interactions. |
| 120 |
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// Dipoles may be either traditional point-dipoles or split-dipoles. |
| 121 |
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// possible formats for a multipolar atom type are: |
| 122 |
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// |
| 123 |
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// Point-dipoles: |
| 124 |
tim |
2102 |
// name d phi theta psi dipole_moment |
| 125 |
gezelter |
2117 |
// |
| 126 |
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// Split-dipoles: |
| 127 |
tim |
2102 |
// name s phi theta psi dipole_moment splitdipole_distance |
| 128 |
gezelter |
2117 |
// |
| 129 |
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// Point-Quadrupoles: |
| 130 |
tim |
2102 |
// name q phi theta psi Qxx Qyy Qzz |
| 131 |
gezelter |
2117 |
// |
| 132 |
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// Atoms with both dipole and quadrupole moments: |
| 133 |
tim |
2102 |
// name dq phi theta psi dipole_moment Qxx Qyy Qzz |
| 134 |
gezelter |
2117 |
// |
| 135 |
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// Atoms with both split dipoles and quadrupole moments: |
| 136 |
tim |
2102 |
// name sq phi theta psi dipole_moment splitdipole_distance Qxx Qyy Qzz |
| 137 |
tim |
2096 |
// |
| 138 |
gezelter |
2117 |
// Euler angles are given in zxz convention in units of degrees. |
| 139 |
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// |
| 140 |
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// Charges are given in units of electrons. |
| 141 |
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// |
| 142 |
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// Dipoles are given in units of Debyes. |
| 143 |
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// |
| 144 |
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// Split dipole distances are given in units of Angstroms. |
| 145 |
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// |
| 146 |
|
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// Quadrupole moments are given in units of 10^-26 esu cm^2 (also known as an |
| 147 |
|
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// esu centi-barn) |
| 148 |
|
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// |
| 149 |
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SSD_E dq 0.0 0.0 0.0 2.42 -1.682 1.762 -0.08 |
| 150 |
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SSD_RF dq 0.0 0.0 0.0 2.48 -1.682 1.762 -0.08 |
| 151 |
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SSD dq 0.0 0.0 0.0 2.35 -1.682 1.762 -0.08 |
| 152 |
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SSD1 dq 0.0 0.0 0.0 2.35 -1.682 1.762 -0.08 |
| 153 |
tim |
2098 |
//HDP s 0.0 0.0 0.0 20.6 4.63 |
| 154 |
tim |
2096 |
end MultipoleAtomTypes |
| 155 |
tim |
1921 |
|
| 156 |
|
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begin StickyAtomTypes |
| 157 |
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//name w0 v0 (kcal/mol) v0p rl (Ang) ru rlp rup |
| 158 |
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SSD_E 0.07715 3.90 3.90 2.40 3.80 2.75 3.35 |
| 159 |
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SSD_RF 0.07715 3.90 3.90 2.40 3.80 2.75 3.35 |
| 160 |
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SSD 0.07715 3.7284 3.7284 2.75 3.35 2.75 4.0 |
| 161 |
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SSD1 0.07715 3.6613 3.6613 2.75 3.35 2.75 4.0 |
| 162 |
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end StickyAtomTypes |
| 163 |
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| 164 |
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| 165 |
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begin BondTypes |
| 166 |
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| 167 |
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//Atom1 Atom2 Fixed |
| 168 |
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//V_Fixed = 0 |
| 169 |
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| 170 |
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//Atom1 Atom2 Harmonic b0 Kb (kcal/mol) |
| 171 |
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//V_Harmonic = 0.5*Kb(b- bo)^2 |
| 172 |
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//Harmonic Examples |
| 173 |
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HEAD CH3 Harmonic 2.75 260 |
| 174 |
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HEAD CH2 Harmonic 2.75 260 |
| 175 |
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HEAD CH Harmonic 2.75 260 |
| 176 |
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HEAD TB1 Harmonic 2.76 260 |
| 177 |
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HEAD TB2 Harmonic 3.20 260 |
| 178 |
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HEAD TB3 Harmonic 3.63 260 |
| 179 |
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CH3 CH3 Harmonic 1.526 260 |
| 180 |
|
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CH3 CH2 Harmonic 1.526 260 |
| 181 |
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CH3 CH Harmonic 1.526 260 |
| 182 |
|
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CH2 CH2 Harmonic 1.526 260 |
| 183 |
|
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CH2 CH Harmonic 1.526 260 |
| 184 |
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CH CH Harmonic 1.526 260 |
| 185 |
|
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TB1 TB1 Harmonic 1.526 260 |
| 186 |
|
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TB2 TB2 Harmonic 2.34 260 |
| 187 |
|
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TB3 TB3 Harmonic 3.12 260 |
| 188 |
|
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TB1 TE1 Harmonic 1.526 260 |
| 189 |
|
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TB2 TE2 Harmonic 2.34 260 |
| 190 |
|
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TB3 TE3 Harmonic 3.12 260 |
| 191 |
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| 192 |
|
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//Atom1 Atom2 Cubic b0 K3 K2 K1 K0 |
| 193 |
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//V_Cubic = K3(b - b0)^3 + K2(b - b0)^2 + K1(b - b0) + K0 |
| 194 |
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| 195 |
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| 196 |
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//Atom1 Atom2 Quartic b0 K4 K3 K2 K1 K0 |
| 197 |
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//V_Quartic = K4(b - b0)^4 + K3(b - b0)^3 + K2(b - b0)^2 + K1(b - b0) + K0 |
| 198 |
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| 199 |
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| 200 |
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//Atom1 Atom2 Polynomial b0 i Ki [j Kj] |
| 201 |
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//V_Quartic = Ki(b - b0)^i + Kj(b - b0)^j + ... |
| 202 |
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| 203 |
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| 204 |
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end BondTypes |
| 205 |
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| 206 |
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begin BendTypes |
| 207 |
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| 208 |
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//Harmonic |
| 209 |
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//Atom1 Atom2 Atom3 Harmonic Theta0 Ktheta |
| 210 |
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//V_Harmonic = 0.5*Ktheta(Theta - Theta0)^2 |
| 211 |
|
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//Ktheta: kcal/mole/rad**2 |
| 212 |
|
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//Theta0: degrees |
| 213 |
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//Harmonic examples |
| 214 |
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// |
| 215 |
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HEAD CH2 HEAD Harmonic 114.0 117.68 |
| 216 |
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HEAD CH2 CH3 Harmonic 114.0 117.68 |
| 217 |
|
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HEAD CH2 CH2 Harmonic 114.0 117.68 |
| 218 |
|
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HEAD TB1 TB1 Harmonic 114.0 117.68 |
| 219 |
|
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HEAD TB2 TB2 Harmonic 114.0 117.68 |
| 220 |
|
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HEAD TB3 TB3 Harmonic 114.0 117.68 |
| 221 |
|
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HEAD CH2 CH Harmonic 114.0 117.68 |
| 222 |
|
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HEAD CH CH3 Harmonic 112.0 117.68 |
| 223 |
|
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HEAD CH CH2 Harmonic 112.0 117.68 |
| 224 |
|
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HEAD CH CH Harmonic 112.0 117.68 |
| 225 |
|
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CH3 CH2 CH3 Harmonic 114.0 117.68 |
| 226 |
|
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CH3 CH2 CH2 Harmonic 114.0 117.68 |
| 227 |
|
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CH3 CH2 CH Harmonic 114.0 117.68 |
| 228 |
|
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CH3 CH CH3 Harmonic 112.0 117.68 |
| 229 |
|
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CH3 CH CH2 Harmonic 112.0 117.68 |
| 230 |
|
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CH3 CH CH Harmonic 112.0 117.68 |
| 231 |
|
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CH2 CH2 CH2 Harmonic 114.0 117.68 |
| 232 |
|
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CH2 CH2 CH Harmonic 114.0 117.68 |
| 233 |
|
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CH2 CH CH2 Harmonic 112.0 117.68 |
| 234 |
|
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CH2 CH CH Harmonic 112.0 117.68 |
| 235 |
|
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CH CH2 CH Harmonic 114.0 117.68 |
| 236 |
|
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CH CH CH Harmonic 112.0 117.68 |
| 237 |
|
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TB1 TB1 TB1 Harmonic 114.0 117.68 |
| 238 |
|
|
TB2 TB2 TB2 Harmonic 114.0 117.68 |
| 239 |
|
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TB3 TB3 TB3 Harmonic 114.0 117.68 |
| 240 |
|
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TE1 TB1 TB1 Harmonic 114.0 117.68 |
| 241 |
|
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TE2 TB2 TB2 Harmonic 114.0 117.68 |
| 242 |
|
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TE3 TB3 TB3 Harmonic 114.0 117.68 |
| 243 |
|
|
|
| 244 |
|
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//GhostBend |
| 245 |
|
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//Atom1 Atom2 GHOST GhostBend Theta0 Ktheta |
| 246 |
|
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//Atom2 must be directional atom |
| 247 |
|
|
//Ghost examples |
| 248 |
|
|
CH2 HEAD GHOST GhostBend 129.783 0.00354 |
| 249 |
|
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CH2 HEAD GHOST GhostBend 90.0 117.68 |
| 250 |
|
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TB1 HEAD GHOST GhostBend 90.0 117.68 |
| 251 |
|
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TB2 HEAD GHOST GhostBend 90.0 117.68 |
| 252 |
|
|
TB3 HEAD GHOST GhostBend 90.0 117.68 |
| 253 |
|
|
|
| 254 |
|
|
//UreyBradley |
| 255 |
|
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//Atom1 Atom2 Atom3 UreyBradley Theta0 Ktheta S0 Kub |
| 256 |
|
|
//V_UreyBradleyBend = Ktheta(Theta - Theta0)^2 + Kub(S - S0)^2 |
| 257 |
|
|
//Ktheta: kcal/mole/rad**2 |
| 258 |
|
|
//Theta0: degrees |
| 259 |
|
|
//Kub: kcal/mole/A**2 |
| 260 |
|
|
//S0: A |
| 261 |
|
|
|
| 262 |
|
|
//Cubic |
| 263 |
|
|
//Atom1 Atom2 Atom3 Cubic Theta0 K3 K2 K1 K0 |
| 264 |
|
|
//V_Cubic = K3(Theta - Theta0)^3 + K2(Theta - Theta0)^2 + K1(Theta - Theta0) + K0 |
| 265 |
|
|
|
| 266 |
|
|
//Quartic |
| 267 |
|
|
//Atom1 Atom2 Atom3 Quartic Theta0 K4 K3 K2 K1 K0 |
| 268 |
|
|
//V_Quartic = K4(Theta - Theta0)^4 + K3(Theta - Theta0)^3 + K2(Theta - Theta0)^2 + K1(Theta - Theta0) + K0 |
| 269 |
|
|
|
| 270 |
|
|
//Polynomial |
| 271 |
|
|
//Atom1 Atom2 Atom3 Polynomial Theta0 i Ki [j Kj] |
| 272 |
|
|
//V_Polynomial = Ki(Theta - Theta0)^i + Kj(Theta - Theta0)^j + ... |
| 273 |
|
|
|
| 274 |
|
|
end BendTypes |
| 275 |
|
|
|
| 276 |
|
|
begin TorsionTypes |
| 277 |
|
|
|
| 278 |
|
|
//Cubic |
| 279 |
|
|
//Atom1 Atom2 Atom3 Atom4 Cubic k3 k2 k1 k0 ( all are kcal/mol ) |
| 280 |
|
|
//V_Cubic = k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0 |
| 281 |
|
|
//Cubic Examples |
| 282 |
|
|
HEAD CH2 CH2 HEAD Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 283 |
|
|
HEAD CH2 CH HEAD Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 284 |
|
|
HEAD CH CH HEAD Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 285 |
|
|
HEAD CH2 CH2 CH3 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 286 |
|
|
HEAD CH2 CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 287 |
|
|
HEAD CH CH2 CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 288 |
|
|
HEAD CH CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 289 |
|
|
HEAD CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 290 |
|
|
HEAD CH2 CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 291 |
|
|
HEAD CH CH2 CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 292 |
|
|
HEAD CH CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 293 |
|
|
HEAD CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 294 |
|
|
HEAD CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 295 |
|
|
HEAD CH CH2 CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 296 |
|
|
HEAD CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 297 |
|
|
HEAD TB1 TB1 TB1 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 298 |
|
|
HEAD TB2 TB2 TB2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 299 |
|
|
HEAD TB3 TB3 TB3 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 300 |
|
|
CH3 CH2 CH2 CH3 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 301 |
|
|
CH3 CH2 CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 302 |
|
|
CH3 CH CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 303 |
|
|
CH3 CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 304 |
|
|
CH3 CH2 CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 305 |
|
|
CH3 CH CH2 CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 306 |
|
|
CH3 CH CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 307 |
|
|
CH3 CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 308 |
|
|
CH3 CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 309 |
|
|
CH3 CH CH2 CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 310 |
|
|
CH3 CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 311 |
|
|
CH2 CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 312 |
|
|
CH2 CH2 CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 313 |
|
|
CH2 CH CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 314 |
|
|
CH2 CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 315 |
|
|
CH2 CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 316 |
|
|
CH2 CH CH2 CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 317 |
|
|
CH2 CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 318 |
|
|
CH CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 319 |
|
|
CH CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 320 |
|
|
CH CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 321 |
|
|
TB1 TB1 TB1 TB1 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 322 |
|
|
TB2 TB2 TB2 TB2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 323 |
|
|
TB3 TB3 TB3 TB3 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 324 |
|
|
TE1 TB1 TB1 TB1 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 325 |
|
|
TE2 TB2 TB2 TB2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 326 |
|
|
TE3 TB3 TB3 TB3 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 327 |
|
|
|
| 328 |
|
|
//Charmm |
| 329 |
|
|
//Atom1 Atom2 Atom3 Atom4 Charmm Kchi n delta [Kchi n delta] |
| 330 |
|
|
//V_Charmm = Kchi(1 + cos(n(chi) - delta)) |
| 331 |
|
|
//Kchi: kcal/mole |
| 332 |
|
|
//n: multiplicity |
| 333 |
|
|
//delta: degrees |
| 334 |
|
|
//in some cases, a Charmm may have two or three terms. If n is equal to 0, it falls back to harmonic form |
| 335 |
|
|
|
| 336 |
|
|
//Quartic |
| 337 |
|
|
//Atom1 Atom2 Atom3 Atom4 Quartic k4 k3 k2 k1 k0 ( all are kcal/mol ) |
| 338 |
|
|
//V_Quartic = k4(cos phi)^4 + k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0 |
| 339 |
|
|
|
| 340 |
|
|
//Polynomial |
| 341 |
|
|
//Atom1 Atom2 Atom3 Atom4 Polynomial i Ki [j Kj] |
| 342 |
|
|
//VPolynomial = Ki (cos phi)^i + ... + Kj (cos phi)^j |
| 343 |
|
|
|
| 344 |
|
|
end TorsionTypes |
| 345 |
|
|
|
| 346 |
|
|
|
