1 |
chuckv |
3156 |
// This is the forcefield file for the Metal-NonMetal(MnM) Interaction Forcefield |
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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6 |
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7 |
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begin Options |
8 |
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Name = "MnM" |
9 |
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MetallicEnergyUnitScaling 23.0605423 |
10 |
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end Options |
11 |
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12 |
chuckv |
3412 |
|
13 |
chuckv |
3156 |
begin AtomTypes |
14 |
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//Name mass (amu) |
15 |
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CH4 16.05 |
16 |
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CH3 15.04 |
17 |
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CH2 14.03 |
18 |
chuckv |
3405 |
CH 13.02 |
19 |
chuckv |
3412 |
// CH3 (sp3) thiol/sulfide/disulfide |
20 |
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CH3S 15.04 |
21 |
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// CH2 (sp3) thiol/sulfide/disulfide |
22 |
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CH2S 14.03 |
23 |
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//CH (sp3) all other/thiol |
24 |
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CHS 13.02 |
25 |
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//C (sp3) all other/thiol |
26 |
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CS 12.0107 |
27 |
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// sulfone |
28 |
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SYZ 32.0655 |
29 |
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// O in sulfone |
30 |
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OY |
31 |
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// thiol S |
32 |
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SH 32.0655 |
33 |
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//Thiol H |
34 |
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HS 1.0079 |
35 |
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// Sulfoxide |
36 |
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SZ 32.0655 |
37 |
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// Sulfur in disulfide |
38 |
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SS 32.0655 |
39 |
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// Sulfur in aromatic (thiophene) |
40 |
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SP 32.0655 |
41 |
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// sp2 carbon in thiophene |
42 |
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CS 12.0107 |
43 |
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// Sulfur attached to gold |
44 |
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SAu 228.9807 |
45 |
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46 |
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//Water |
47 |
chuckv |
3156 |
SSD 18.0153 |
48 |
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SSD1 18.0153 |
49 |
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SSD_E 18.0153 |
50 |
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SSD_RF 18.0153 |
51 |
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O_TIP3P 15.9994 |
52 |
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O_TIP4P 15.9994 |
53 |
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O_TIP4P-Ew 15.9994 |
54 |
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O_TIP5P 15.9994 |
55 |
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O_TIP5P-E 15.9994 |
56 |
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O_SPCE 15.9994 |
57 |
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O_SPC 15.9994 |
58 |
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H_TIP3P 1.0079 |
59 |
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H_TIP4P 1.0079 |
60 |
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H_TIP4P-Ew 1.0079 |
61 |
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H_TIP5P 1.0079 |
62 |
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H_SPCE 1.0079 |
63 |
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H_SPC 1.0079 |
64 |
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EP_TIP4P 0.0 |
65 |
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EP_TIP4P-Ew 0.0 |
66 |
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EP_TIP5P 0.0 |
67 |
chuckv |
3412 |
|
68 |
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//Standard Atoms |
69 |
chuckv |
3156 |
C 12.0107 |
70 |
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S 32.0655 |
71 |
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Ni 58.710 |
72 |
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Cu 63.550 |
73 |
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Rh 102.90550 |
74 |
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Pd 106.42 |
75 |
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Ag 107.8682 |
76 |
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Ir 192.217 |
77 |
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Pt 195.09 |
78 |
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Au 196.97 |
79 |
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end AtomTypes |
80 |
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81 |
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begin DirectionalAtomTypes |
82 |
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//Name I_xx I_yy I_zz (All moments in (amu*Ang^2) |
83 |
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SSD 1.7696 0.6145 1.1550 |
84 |
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SSD1 1.7696 0.6145 1.1550 |
85 |
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SSD_E 1.7696 0.6145 1.1550 |
86 |
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SSD_RF 1.7696 0.6145 1.1550 |
87 |
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end DirectionalAtomTypes |
88 |
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89 |
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90 |
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begin LennardJonesAtomTypes |
91 |
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//Name epsilon sigma |
92 |
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SSD 0.152 3.051 |
93 |
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SSD1 0.152 3.016 |
94 |
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SSD_E 0.152 3.035 |
95 |
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SSD_RF 0.152 3.019 |
96 |
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O_TIP3P 0.1521 3.15061 |
97 |
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O_TIP4P 0.1550 3.15365 |
98 |
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O_TIP4P-Ew 0.16275 3.16435 |
99 |
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O_TIP5P 0.16 3.12 |
100 |
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O_TIP5P-E 0.178 3.097 |
101 |
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O_SPCE 0.15532 3.16549 |
102 |
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O_SPC 0.15532 3.16549 |
103 |
chuckv |
3412 |
// From TraPPE-UA JPCB, 109, 24100 and JCPB 102,2569 |
104 |
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CH4 0.2941 3.73 |
105 |
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CH3 0.1947 3.75 |
106 |
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CH2 0.09140 3.95 |
107 |
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CH 0.0987 4.68 |
108 |
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CS 0.0009935 6.40 |
109 |
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CH3S 0.1947 3.75 |
110 |
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CH2S 0.09140 3.95 |
111 |
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CHS 0.0987 4.68 |
112 |
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S 0.3954 3.58 |
113 |
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SH 0.4610 3.62 |
114 |
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SS 0.3279 3.72 |
115 |
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SP 0.3576 3.60 |
116 |
chuckv |
3156 |
end LennardJonesAtomTypes |
117 |
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|
118 |
chuckv |
3161 |
begin SCAtomTypes |
119 |
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// Name epsilon(eV) c m n alpha(angstroms) |
120 |
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Ni 0.0073767 84.745 5.0 10.0 3.5157 |
121 |
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Cu 0.0057921 84.843 5.0 10.0 3.6030 |
122 |
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Rh 0.0024612 305.499 5.0 13.0 3.7984 |
123 |
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Pd 0.0032864 148.205 6.0 12.0 3.8813 |
124 |
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Ag 0.0039450 96.524 6.0 11.0 4.0691 |
125 |
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Ir 0.0037674 224.815 6.0 13.0 3.8344 |
126 |
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Pt 0.0097894 71.336 7.0 11.0 3.9163 |
127 |
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Au 0.0078052 53.581 8.0 11.0 4.0651 |
128 |
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end SCAtomTypes |
129 |
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130 |
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131 |
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// Metal non-metal interactions. |
132 |
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// Format: Metal Atom Type, Non-Metal Atom Type, Interaction Type, Interaction Parameters |
133 |
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// Where interaction type can be: MAW, LennardJones or ShiftedMorse or RepulsiveMorse |
134 |
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begin MetalNonMetalInteractions |
135 |
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136 |
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//MAW (Metal Angular Water section) |
137 |
chuckv |
3392 |
// r_e, D_e beta ca1 cb1 |
138 |
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Cu SSD_E MAW 2.5525 1.9850 1.1680 1.1250 0.750000 |
139 |
chuckv |
3356 |
//Au SSD_E MAW 2.8170 1.7850 1.2680 1.2500 0.2050 0.0 |
140 |
chuckv |
3392 |
//Au SSD_E MAW 2.7510 2.95 1.101 0.750000 0.750000 |
141 |
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//1. 1.5 2.6500001 -3.000162356E-2 1.30999744 |
142 |
chuckv |
3397 |
//Au SSD_E MAW 2.7 1.06 1.264 0.16 0.8 |
143 |
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Au SSD_E MAW 2.68 0.6 1.33 0.95 -0.25 |
144 |
chuckv |
3161 |
|
145 |
|
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//LennardJones |
146 |
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// sigma epsilon |
147 |
chuckv |
3409 |
Au CH3 LennardJones 3.54 0.2146 |
148 |
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Au CH2 LennardJones 3.54 0.1749 |
149 |
chuckv |
3407 |
Au S LennardJones 4.45 9.180 |
150 |
chuckv |
3161 |
|
151 |
|
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//Shifted Morse |
152 |
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// r0 D0 beta0 |
153 |
chuckv |
3356 |
Au O_SPCE ShiftedMorse 3.70 0.0424 0.769 |
154 |
chuckv |
3161 |
|
155 |
|
|
//Repulsive Morse |
156 |
|
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// r0 D0 beta0 |
157 |
chuckv |
3356 |
Au H_SPCE RepulsiveMorse -1.00 0.00850 0.769 |
158 |
chuckv |
3161 |
|
159 |
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160 |
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end MetalNonMetalInteractions |
161 |
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162 |
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|
163 |
chuckv |
3156 |
begin ChargeAtomTypes |
164 |
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// Name charge |
165 |
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O_TIP3P -0.834 |
166 |
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O_SPCE -0.8476 |
167 |
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O_SPC -0.82 |
168 |
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H_TIP3P 0.417 |
169 |
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H_TIP4P 0.520 |
170 |
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H_TIP4P-Ew 0.52422 |
171 |
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H_TIP5P 0.241 |
172 |
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H_SPCE 0.4238 |
173 |
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H_SPC 0.42 |
174 |
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EP_TIP4P -1.040 |
175 |
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EP_TIP4P-Ew -1.04844 |
176 |
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EP_TIP5P -0.241 |
177 |
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end ChargeAtomTypes |
178 |
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179 |
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begin MultipoleAtomTypes |
180 |
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// OOPSE currently only supports charge-charge, charge-dipole, |
181 |
|
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// dipole-dipole, and charge-quadrupole interactions. |
182 |
|
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// Dipoles may be either traditional point-dipoles or split-dipoles. |
183 |
|
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// possible formats for a multipolar atom type are: |
184 |
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// |
185 |
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// Point-dipoles: |
186 |
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// name d phi theta psi dipole_moment |
187 |
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// |
188 |
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// Split-dipoles: |
189 |
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// name s phi theta psi dipole_moment splitdipole_distance |
190 |
|
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// |
191 |
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// Point-Quadrupoles: |
192 |
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// name q phi theta psi Qxx Qyy Qzz |
193 |
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// |
194 |
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// Atoms with both dipole and quadrupole moments: |
195 |
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// name dq phi theta psi dipole_moment Qxx Qyy Qzz |
196 |
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// |
197 |
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// Atoms with both split dipoles and quadrupole moments: |
198 |
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// name sq phi theta psi dipole_moment splitdipole_distance Qxx Qyy Qzz |
199 |
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// |
200 |
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// Euler angles are given in zxz convention in units of degrees. |
201 |
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// |
202 |
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// Charges are given in units of electrons. |
203 |
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// |
204 |
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// Dipoles are given in units of Debyes. |
205 |
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// |
206 |
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// Split dipole distances are given in units of Angstroms. |
207 |
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// |
208 |
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// Quadrupole moments are given in units of 10^-26 esu cm^2 (also known as an |
209 |
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// esu centi-barn) |
210 |
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// |
211 |
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SSD_E dq 0.0 0.0 0.0 2.42 -1.682 1.762 -0.08 |
212 |
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SSD_RF dq 0.0 0.0 0.0 2.48 -1.682 1.762 -0.08 |
213 |
|
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SSD dq 0.0 0.0 0.0 2.35 -1.682 1.762 -0.08 |
214 |
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SSD1 dq 0.0 0.0 0.0 2.35 -1.682 1.762 -0.08 |
215 |
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end MultipoleAtomTypes |
216 |
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|
217 |
|
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begin StickyAtomTypes |
218 |
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//name w0 v0 (kcal/mol) v0p rl (Ang) ru rlp rup |
219 |
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SSD_E 0.07715 3.90 3.90 2.40 3.80 2.75 3.35 |
220 |
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SSD_RF 0.07715 3.90 3.90 2.40 3.80 2.75 3.35 |
221 |
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SSD 0.07715 3.7284 3.7284 2.75 3.35 2.75 4.0 |
222 |
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SSD1 0.07715 3.6613 3.6613 2.75 3.35 2.75 4.0 |
223 |
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end StickyAtomTypes |
224 |
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225 |
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226 |
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begin BondTypes |
227 |
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228 |
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//Atom1 Atom2 Fixed |
229 |
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//V_Fixed = 0 |
230 |
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|
231 |
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//Atom1 Atom2 Harmonic b0 Kb (kcal/mol) |
232 |
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//V_Harmonic = 0.5*Kb(b- bo)^2 |
233 |
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//Harmonic Examples |
234 |
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CH3 CH3 Harmonic 1.526 260 |
235 |
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CH3 CH2 Harmonic 1.526 260 |
236 |
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CH3 CH Harmonic 1.526 260 |
237 |
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CH2 CH2 Harmonic 1.526 260 |
238 |
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CH2 CH Harmonic 1.526 260 |
239 |
|
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CH CH Harmonic 1.526 260 |
240 |
kfletche |
3411 |
// fix the Kb for the thiol below: |
241 |
chuckv |
3412 |
S CH2 Harmonic 1.82 281 |
242 |
chuckv |
3156 |
|
243 |
|
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//Atom1 Atom2 Cubic b0 K3 K2 K1 K0 |
244 |
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//V_Cubic = K3(b - b0)^3 + K2(b - b0)^2 + K1(b - b0) + K0 |
245 |
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|
246 |
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|
247 |
|
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//Atom1 Atom2 Quartic b0 K4 K3 K2 K1 K0 |
248 |
|
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//V_Quartic = K4(b - b0)^4 + K3(b - b0)^3 + K2(b - b0)^2 + K1(b - b0) + K0 |
249 |
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|
250 |
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|
251 |
|
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//Atom1 Atom2 Polynomial b0 i Ki [j Kj] |
252 |
|
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//V_Quartic = Ki(b - b0)^i + Kj(b - b0)^j + ... |
253 |
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254 |
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255 |
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end BondTypes |
256 |
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257 |
|
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begin BendTypes |
258 |
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|
259 |
|
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//Harmonic |
260 |
|
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//Atom1 Atom2 Atom3 Harmonic Theta0 Ktheta |
261 |
|
|
//V_Harmonic = 0.5*Ktheta(Theta - Theta0)^2 |
262 |
|
|
//Ktheta: kcal/mole/rad**2 |
263 |
|
|
//Theta0: degrees |
264 |
|
|
//Harmonic examples |
265 |
|
|
// |
266 |
|
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CH3 CH2 CH3 Harmonic 114.0 117.68 |
267 |
|
|
CH3 CH2 CH2 Harmonic 114.0 117.68 |
268 |
|
|
CH3 CH2 CH Harmonic 114.0 117.68 |
269 |
|
|
CH3 CH CH3 Harmonic 112.0 117.68 |
270 |
|
|
CH3 CH CH2 Harmonic 112.0 117.68 |
271 |
|
|
CH3 CH CH Harmonic 112.0 117.68 |
272 |
|
|
CH2 CH2 CH2 Harmonic 114.0 117.68 |
273 |
|
|
CH2 CH2 CH Harmonic 114.0 117.68 |
274 |
|
|
CH2 CH CH2 Harmonic 112.0 117.68 |
275 |
|
|
CH2 CH CH Harmonic 112.0 117.68 |
276 |
|
|
CH CH2 CH Harmonic 114.0 117.68 |
277 |
|
|
CH CH CH Harmonic 112.0 117.68 |
278 |
chuckv |
3410 |
S CH2 CH2 Harmonic 114.0 117.68 |
279 |
chuckv |
3156 |
|
280 |
|
|
|
281 |
|
|
//UreyBradley |
282 |
|
|
//Atom1 Atom2 Atom3 UreyBradley Theta0 Ktheta S0 Kub |
283 |
|
|
//V_UreyBradleyBend = Ktheta(Theta - Theta0)^2 + Kub(S - S0)^2 |
284 |
|
|
//Ktheta: kcal/mole/rad**2 |
285 |
|
|
//Theta0: degrees |
286 |
|
|
//Kub: kcal/mole/A**2 |
287 |
|
|
//S0: A |
288 |
|
|
|
289 |
|
|
//Cubic |
290 |
|
|
//Atom1 Atom2 Atom3 Cubic Theta0 K3 K2 K1 K0 |
291 |
|
|
//V_Cubic = K3(Theta - Theta0)^3 + K2(Theta - Theta0)^2 + K1(Theta - Theta0) + K0 |
292 |
|
|
|
293 |
|
|
//Quartic |
294 |
|
|
//Atom1 Atom2 Atom3 Quartic Theta0 K4 K3 K2 K1 K0 |
295 |
|
|
//V_Quartic = K4(Theta - Theta0)^4 + K3(Theta - Theta0)^3 + K2(Theta - Theta0)^2 + K1(Theta - Theta0) + K0 |
296 |
|
|
|
297 |
|
|
//Polynomial |
298 |
|
|
//Atom1 Atom2 Atom3 Polynomial Theta0 i Ki [j Kj] |
299 |
|
|
//V_Polynomial = Ki(Theta - Theta0)^i + Kj(Theta - Theta0)^j + ... |
300 |
|
|
|
301 |
|
|
end BendTypes |
302 |
|
|
|
303 |
|
|
begin TorsionTypes |
304 |
|
|
|
305 |
kfletche |
3411 |
// All thiol torsions from Kautman and Klein (J. Phys. Chem. 1989, 91, 4994-5001) |
306 |
|
|
|
307 |
chuckv |
3412 |
//S CH2 CH2 CH3 Polynomial 0 2.218 1 2.905 2 -3.136 3 -0.7313 4 6.272 5 -7.528 |
308 |
|
|
//S CH2 CH2 CH2 Polynomial 0 2.218 1 2.905 2 -3.136 3 -0.7313 4 6.272 5 -7.528 |
309 |
|
|
//S CH2 CH2 CH Polynomial 0 2.218 1 2.905 2 -3.136 3 -0.7313 4 6.272 5 -7.528 |
310 |
|
|
//S CH2 CH2 C Polynomial 0 2.218 1 2.905 2 -3.136 3 -0.7313 4 6.272 5 -7.528 |
311 |
kfletche |
3411 |
|
312 |
|
|
// All type 1 possibilities from Dubbeldam et al. (J. Phys. Chem. B 2004, 108, 12301-12313) |
313 |
|
|
|
314 |
chuckv |
3412 |
//CH3 CH2 CH2 CH3 Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
315 |
|
|
//CH3 CH2 CH2 CH2 Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
316 |
|
|
//CH3 CH2 CH2 CH Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
317 |
|
|
//CH3 CH2 CH2 C Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
318 |
|
|
//CH2 CH2 CH2 CH2 Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
319 |
|
|
//CH2 CH2 CH2 CH Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
320 |
|
|
//CH2 CH2 CH2 C Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
321 |
|
|
//CH CH2 CH2 CH Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
322 |
|
|
//CH CH2 CH2 C Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
323 |
|
|
//C CH2 CH2 C Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
324 |
kfletche |
3411 |
|
325 |
|
|
// All type 2 possibilities: |
326 |
|
|
|
327 |
chuckv |
3412 |
//H CH CH2 CH3 Polynomial 0 2.7167 1 8.665 2 0.82669 3 -12.92 4 -1.653 5 3.2712 |
328 |
|
|
//H CH CH2 CH2 Polynomial 0 2.7161 1 8.665 2 0.82669 3 -12.92 4 -1.653 5 3.2712 |
329 |
|
|
//H CH CH2 CH Polynomial 0 2.7161 1 8.665 2 0.82669 3 -12.92 4 -1.653 5 3.2712 |
330 |
|
|
//H CH CH2 C Polynomial 0 2.7161 1 8.665 2 0.82669 3 -12.92 4 -1.653 5 3.2712 |
331 |
kfletche |
3411 |
|
332 |
|
|
// All type 3 possibilities: |
333 |
|
|
|
334 |
chuckv |
3412 |
//CH3 C CH2 CH3 Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
335 |
|
|
//CH3 C CH2 CH2 Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
336 |
|
|
//CH3 C CH2 CH Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
337 |
|
|
//CH3 C CH2 C Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
338 |
|
|
//CH2 C CH2 CH2 Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
339 |
|
|
//CH2 C CH2 CH Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
340 |
|
|
//CH2 C CH2 C Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
341 |
|
|
//CH C CH2 CH Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
342 |
|
|
//CH C CH2 C Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
343 |
|
|
//C C CH2 C Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
344 |
kfletche |
3411 |
|
345 |
|
|
// All type 4 possibilities: |
346 |
|
|
|
347 |
chuckv |
3412 |
//CH3 C C CH3 Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
348 |
|
|
//CH3 C C CH2 Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
349 |
|
|
//CH3 C C CH Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
350 |
|
|
//CH3 C C C Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
351 |
|
|
//CH2 C C CH2 Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
352 |
|
|
//CH2 C C CH Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
353 |
|
|
//CH2 C C C Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
354 |
|
|
//CH C C CH Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
355 |
|
|
//CH C C C Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
356 |
|
|
//C C C C Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
357 |
kfletche |
3411 |
|
358 |
|
|
//All type 5 possibilities: |
359 |
|
|
|
360 |
chuckv |
3412 |
//CH3 C CH H Polynomial 0 3.1301 1 9.390 2 0 3 -12.52 4 0 5 0 |
361 |
|
|
//CH2 C CH H Polynomial 0 3.1301 1 9.390 2 0 3 -12.52 4 0 5 0 |
362 |
|
|
//CH C CH H Polynomial 0 3.1301 1 9.390 2 0 3 -12.52 4 0 5 0 |
363 |
|
|
//C C CH H Polynomial 0 3.1301 1 9.390 2 0 3 -12.52 4 0 5 0 |
364 |
kfletche |
3411 |
|
365 |
|
|
//All type 6 possibilities: |
366 |
|
|
|
367 |
chuckv |
3412 |
//H CH CH H Polynomial 0 2.1706 1 5.609 2 -1.804 3 -5.976 4 3.6089 5 -3.6089 |
368 |
kfletche |
3411 |
|
369 |
chuckv |
3156 |
//Cubic |
370 |
|
|
//Atom1 Atom2 Atom3 Atom4 Cubic k3 k2 k1 k0 ( all are kcal/mol ) |
371 |
|
|
//V_Cubic = k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0 |
372 |
|
|
//Cubic Examples |
373 |
chuckv |
3412 |
CH3 CH2 CH2 CH3 Cubic 5.9602 -0.2568 -3.802 2.1586 |
374 |
|
|
CH3 CH2 CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
375 |
|
|
CH3 CH CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
376 |
|
|
CH3 CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
377 |
|
|
CH3 CH2 CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
378 |
|
|
CH3 CH CH2 CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
379 |
|
|
CH3 CH CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
380 |
|
|
CH3 CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
381 |
|
|
CH3 CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
382 |
|
|
CH3 CH CH2 CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
383 |
|
|
CH3 CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
384 |
|
|
CH2 CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
385 |
|
|
CH2 CH2 CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
386 |
|
|
CH2 CH CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
387 |
|
|
CH2 CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
388 |
|
|
CH2 CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
389 |
|
|
CH2 CH CH2 CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
390 |
|
|
CH2 CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
391 |
|
|
CH CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
392 |
|
|
CH CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
393 |
|
|
CH CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
394 |
|
|
S CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
395 |
chuckv |
3156 |
|
396 |
chuckv |
3412 |
//Opls |
397 |
gezelter |
3413 |
//Atom1 Atom2 Atom3 Atom4 Opls v1 v2 v3 |
398 |
|
|
//V_Opls = v1 / 2 * [1 + cos(phi)] + v2 / 2 * [1 - cos(2*phi)] + v3 / 2 * [1 + cos(3*phi)] |
399 |
chuckv |
3412 |
//units for v_n: kcal / mol |
400 |
|
|
|
401 |
gezelter |
3413 |
//Trappe |
402 |
|
|
//Atom1 Atom2 Atom3 Atom4 Trappe c0 c1 c2 c3 |
403 |
|
|
//V_Opls = c0 + c1 * [1 + cos(phi)] + c2 * [1 - cos(2*phi)] + c3 * [1 + cos(3*phi)] |
404 |
|
|
//units for c_n: kcal / mol |
405 |
chuckv |
3412 |
|
406 |
chuckv |
3156 |
//Charmm |
407 |
|
|
//Atom1 Atom2 Atom3 Atom4 Charmm Kchi n delta [Kchi n delta] |
408 |
|
|
//V_Charmm = Kchi(1 + cos(n(chi) - delta)) |
409 |
|
|
//Kchi: kcal/mole |
410 |
|
|
//n: multiplicity |
411 |
|
|
//delta: degrees |
412 |
|
|
//in some cases, a Charmm may have two or three terms. If n is equal to 0, it falls back to harmonic form |
413 |
|
|
|
414 |
|
|
//Quartic |
415 |
|
|
//Atom1 Atom2 Atom3 Atom4 Quartic k4 k3 k2 k1 k0 ( all are kcal/mol ) |
416 |
|
|
//V_Quartic = k4(cos phi)^4 + k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0 |
417 |
|
|
|
418 |
|
|
//Polynomial |
419 |
|
|
//Atom1 Atom2 Atom3 Atom4 Polynomial i Ki [j Kj] |
420 |
|
|
//VPolynomial = Ki (cos phi)^i + ... + Kj (cos phi)^j |
421 |
|
|
|
422 |
|
|
end TorsionTypes |
423 |
|
|
|
424 |
|
|
|