1 |
begin AtomTypes |
2 |
//Name mass (amu) |
3 |
CH4 16.05 |
4 |
CH3 15.04 |
5 |
CH2 14.03 |
6 |
CH 13.02 |
7 |
CE 28.01 //C-O |
8 |
CK 28.01 //C=O |
9 |
HDP 14.03 //Head Dipole |
10 |
NC4 73.137 //CH2-N(CH3)3 |
11 |
PO4 108.995 //PO4-CH2 |
12 |
SSD 18.0153 |
13 |
SSD1 18.0153 |
14 |
SSD_E 18.0153 |
15 |
SSD_RF 18.0153 |
16 |
end AtomTypes |
17 |
|
18 |
|
19 |
|
20 |
begin DirectionalAtomTypes |
21 |
//Name I_xx I_yy I_zz (All moments in (amu*Ang^2) |
22 |
SSD 1.7696 0.6145 1.1550 |
23 |
SSD1 1.7696 0.6145 1.1550 |
24 |
SSD_E 1.7696 0.6145 1.1550 |
25 |
SSD_RF 1.7696 0.6145 1.1550 |
26 |
HDP 2.221 0.0 2.221 |
27 |
CE 13.643 13.643 0.0 |
28 |
CK 10.161 10.161 0.0 |
29 |
end DirectionalAtomTypes |
30 |
|
31 |
begin LennardJonesAtomTypes |
32 |
//Name epsilon sigma |
33 |
SSD 0.152 3.051 |
34 |
SSD1 0.152 3.016 |
35 |
SSD_E 0.152 3.035 |
36 |
SSD_RF 0.152 3.019 |
37 |
|
38 |
//CH3 3.75 98.0 |
39 |
//CH2 3.94 46.0 |
40 |
//CH 4.33 10.0 |
41 |
CH3 0.195 3.75 |
42 |
CH2 0.0914 3.95 |
43 |
CH 0.0199 4.68 |
44 |
CK 0.311 3.592 |
45 |
CE 0.294 3.427 |
46 |
PO4 0.543 4.55 |
47 |
NC4 1.1 4.11 |
48 |
HDP 0.0914 3.95 |
49 |
end LennardJonesAtomTypes |
50 |
|
51 |
begin ChargeAtomTypes |
52 |
// name charge |
53 |
end ChargeAtomTypes |
54 |
|
55 |
begin MultipoleAtomTypes |
56 |
//only support up tp quadrupole. |
57 |
//possible format: |
58 |
// name d theta phi psi dipole_moment |
59 |
// name s theta phi psi dipole_moment splitdipole_distance |
60 |
// name q theta phi psi Qxx Qyy Qzz |
61 |
// name dq theta phi psi dipole_moment Qxx Qyy Qzz |
62 |
// name sq theta phi psi dipole_moment splitdipole_distance Qxx Qyy Qzz |
63 |
// euler angles are given in units of degree |
64 |
// dipoles are given in units of Debye |
65 |
// split dipole distances are given in units of Angstrom |
66 |
// quadrupoles are given in units of |
67 |
// |
68 |
SSD_E d 0.0 0.0 0.0 2.42 |
69 |
SSD_RF d 0.0 0.0 0.0 2.48 |
70 |
SSD d 0.0 0.0 0.0 2.35 |
71 |
SSD1 d 0.0 0.0 0.0 2.35 |
72 |
CE d 0.0 0.0 0.0 1.693 |
73 |
CK d 0.0 0.0 0.0 2.478 |
74 |
HDP s 0.0 0.0 0.0 20.6 4.63 |
75 |
end MultipoleAtomTypes |
76 |
|
77 |
|
78 |
begin BondTypes |
79 |
|
80 |
//Atom1 Atom2 Fixed |
81 |
//V_Fixed = 0 |
82 |
|
83 |
//Atom1 Atom2 Harmonic b0 Kb (kcal/mol) |
84 |
//V_Harmonic = 0.5*Kb(b- bo)^2 |
85 |
//Harmonic Examples |
86 |
|
87 |
//CHx-CHy 1.54 |
88 |
CH3 CH3 Harmonic 1.54 260 |
89 |
CH3 CH2 Harmonic 1.54 260 |
90 |
CH3 CH Harmonic 1.54 260 |
91 |
CH2 CH2 Harmonic 1.54 260 |
92 |
CH2 CH Harmonic 1.54 260 |
93 |
CH CH Harmonic 1.54 260 |
94 |
|
95 |
PO4 CH2 Harmonic 2.67 260 |
96 |
CH2 CE Harmonic 1.54 260 |
97 |
CE CE Harmonic 2.27 260 |
98 |
CE CK Harmonic 2.08 317 |
99 |
|
100 |
//CHx-C aldehyde/ketone 1.52 |
101 |
CH3 CK Harmonic 1.52 317 |
102 |
CH2 CK Harmonic 1.52 317 |
103 |
CH CK Harmonic 1.52 317 |
104 |
|
105 |
end BondTypes |
106 |
|
107 |
begin BendTypes |
108 |
|
109 |
//Harmonic |
110 |
//Atom1 Atom2 Atom3 Harmonic Theta0 Ktheta |
111 |
//V_Harmonic = 0.5*Ktheta(Theta - Theta0)^2 |
112 |
//Ktheta: kcal/mole/rad**2 |
113 |
//Theta0: degrees |
114 |
//Harmonic examples |
115 |
|
116 |
//CHx-CH2-CHy 114 62500 (ktheta/kb) |
117 |
CH3 CH2 CH3 Harmonic 114.0 124.15 |
118 |
CH3 CH2 CH2 Harmonic 114.0 124.15 |
119 |
CH3 CH2 CH Harmonic 114.0 124.15 |
120 |
CH2 CH2 CH2 Harmonic 114.0 124.15 |
121 |
CH2 CH2 CH Harmonic 114.0 124.15 |
122 |
CH CH2 CH Harmonic 114.0 124.15 |
123 |
|
124 |
//CHx-CH-CHy 112 62500 (ktheta/kb) |
125 |
CH3 CH CH3 Harmonic 112.0 124.15 |
126 |
CH3 CH CH2 Harmonic 112.0 124.15 |
127 |
CH3 CH CH Harmonic 112.0 124.15 |
128 |
CH2 CH CH3 Harmonic 112.0 124.15 |
129 |
CH2 CH CH2 Harmonic 112.0 124.15 |
130 |
CH2 CH CH Harmonic 112.0 124.15 |
131 |
CH CH CH3 Harmonic 112.0 124.15 |
132 |
CH CH CH2 Harmonic 112.0 124.15 |
133 |
CH CH CH Harmonic 112.0 124.15 |
134 |
|
135 |
//CHx-C(=O)-CHy 117.2 62500 |
136 |
CH3 CK CH3 Harmonic 117.2 124.15 |
137 |
CH3 CK CH2 Harmonic 117.2 124.15 |
138 |
CH3 CK CH Harmonic 117.2 124.15 |
139 |
CH2 CK CH2 Harmonic 117.2 124.15 |
140 |
CH2 CK CH Harmonic 117.2 124.15 |
141 |
CH CK CH Harmonic 117.2 124.15 |
142 |
CE CK CH3 Harmonic 117.2 124.15 |
143 |
CE CK CH2 Harmonic 117.2 124.15 |
144 |
CE CK CH Harmonic 117.2 124.15 |
145 |
|
146 |
CH2 CH2 CK Harmonic 114 124.15 |
147 |
CE CE CK Harmonic 114 124.15 |
148 |
CH2 CE CE Harmonic 117.2 124.15 |
149 |
CH2 CE CK Harmonic 114 124.15 |
150 |
|
151 |
PO4 CH2 CE Harmonic 180.0 124.15 |
152 |
//GhostBend |
153 |
//Atom1 Atom2 GHOST GhostBend Theta0 Ktheta |
154 |
//Atom2 must be directional atom |
155 |
//Ghost examples |
156 |
CH2 HDP GHOST GhostBend 129.783 0.00354 |
157 |
NC4 PO4 CH2 Harmonic 98.03 20.00 |
158 |
//CHx-C=O 121.4 62500 |
159 |
//since the dipole direction is from Oxygen to carbon in CK |
160 |
//The equilibrium angle becomes its supplementary angle |
161 |
CH3 CK GHOST GhostBend 58.6 124.15 |
162 |
CH2 CK GHOST GhostBend 58.6 124.15 |
163 |
CH CK GHOST GhostBend 58.6 124.15 |
164 |
CH2 CE GHOST GhostBend 68.0 119.98 |
165 |
end BendTypes |
166 |
|
167 |
begin TorsionTypes |
168 |
|
169 |
//Cubic |
170 |
//Atom1 Atom2 Atom3 Atom4 Cubic k3 k2 k1 k0 ( all are kcal/mol ) |
171 |
//V_Cubic = k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0 |
172 |
//Cubic Examples |
173 |
//CHx-CH2-CH2-CHy 0 335.05 -68.19 791.32 |
174 |
CH3 CH2 CH2 CH3 Cubic 6.287 0.2709 -4.050 2.237 |
175 |
CH3 CH2 CH CH3 Cubic 6.287 0.2709 -4.050 2.237 |
176 |
CH3 CH CH CH3 Cubic 6.287 0.2709 -4.050 2.237 |
177 |
CH3 CH2 CH2 CH2 Cubic 6.287 0.2709 -4.050 2.237 |
178 |
CH3 CH2 CH CH2 Cubic 6.287 0.2709 -4.050 2.237 |
179 |
CH3 CH CH2 CH2 Cubic 6.287 0.2709 -4.050 2.237 |
180 |
CH3 CH CH CH2 Cubic 6.287 0.2709 -4.050 2.237 |
181 |
CH3 CH2 CH2 CH Cubic 6.287 0.2709 -4.050 2.237 |
182 |
CH3 CH2 CH CH Cubic 6.287 0.2709 -4.050 2.237 |
183 |
CH3 CH CH2 CH Cubic 6.287 0.2709 -4.050 2.237 |
184 |
CH3 CH CH CH Cubic 6.287 0.2709 -4.050 2.237 |
185 |
CH2 CH2 CH2 CH2 Cubic 6.287 0.2709 -4.050 2.237 |
186 |
CH2 CH2 CH CH2 Cubic 6.287 0.2709 -4.050 2.237 |
187 |
CH2 CH CH CH2 Cubic 6.287 0.2709 -4.050 2.237 |
188 |
CH2 CH2 CH2 CH Cubic 6.287 0.2709 -4.050 2.237 |
189 |
CH2 CH2 CH CH Cubic 6.287 0.2709 -4.050 2.237 |
190 |
CH2 CH CH2 CH Cubic 6.287 0.2709 -4.050 2.237 |
191 |
CH2 CH CH CH Cubic 6.287 0.2709 -4.050 2.237 |
192 |
CH CH2 CH2 CH Cubic 6.287 0.2709 -4.050 2.237 |
193 |
CH CH2 CH CH Cubic 6.287 0.2709 -4.050 2.237 |
194 |
CH CH CH CH Cubic 6.287 0.2709 -4.050 2.237 |
195 |
CK CH2 CH2 CH2 Cubic 6.287 0.2709 -4.050 2.237 |
196 |
|
197 |
//CHx-CH2-CH2-O 0 176.62 -53.34 769.93 |
198 |
CE CK CH2 CH2 Cubic 6.118 0.212 -4.237 1.668 |
199 |
CH2 CE CE GHOST GhostTorsion 6.118 0.212 -4.237 1.668 |
200 |
CH2 CE CK GHOST GhostTorsion 6.118 0.212 -4.237 1.668 |
201 |
|
202 |
//CHx-CHy-C=O 2035.58 -736.90 57.84 -293.23 |
203 |
CH3 CH2 CK GHOST GhostTorsion -2.330 -0.230 0.284 2.227 |
204 |
CH3 CH CK GHOST GhostTorsion -2.330 -0.230 0.284 2.227 |
205 |
CH2 CH2 CK GHOST GhostTorsion -2.330 -0.230 0.284 2.227 |
206 |
CH CH CK GHOST GhostTorsion -2.330 -0.230 0.284 2.227 |
207 |
|
208 |
end TorsionTypes |
209 |
|
210 |
|