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