1 |
molecule{ |
2 |
|
3 |
name = "beadLipid_1G"; |
4 |
nAtoms = 10; |
5 |
|
6 |
atom[0]{ |
7 |
type = "HEAD"; |
8 |
position( -1.503, 0.0, 2.315 ); |
9 |
orientation( 180.0, 90.0, 0.0 ); |
10 |
} |
11 |
atom[1]{ |
12 |
type = "TB1"; |
13 |
position( 0.0, 0.0, 0.0 ); |
14 |
} |
15 |
atom[2]{ |
16 |
type = "TB1"; |
17 |
position( -0.850, 0.0, -1.308 ); |
18 |
} |
19 |
atom[3]{ |
20 |
type = "TB1"; |
21 |
position( 0.0, 0.0, -2.616 ); |
22 |
} |
23 |
atom[4]{ |
24 |
type = "TB1"; |
25 |
position( -0.85, 0.0, -3.924 ); |
26 |
} |
27 |
atom[5]{ |
28 |
type = "TB1"; |
29 |
position( 0.0, 0.0, -5.232 ); |
30 |
} |
31 |
atom[6]{ |
32 |
type = "TB1"; |
33 |
position( -0.85, 0.0, -6.54 ); |
34 |
} |
35 |
atom[7]{ |
36 |
type = "TB1"; |
37 |
position( 0.0, 0.0, -7.848 ); |
38 |
} |
39 |
atom[8]{ |
40 |
type = "TB1"; |
41 |
position( -0.85, 0.0, -9.156 ); |
42 |
} |
43 |
atom[9]{ |
44 |
type = "TE1"; |
45 |
position( 0.0, 0.0, -10.464 ); |
46 |
} |
47 |
|
48 |
nBonds = 9; |
49 |
|
50 |
bond[0]{ |
51 |
members( 0, 1 ); |
52 |
} |
53 |
bond[1]{ |
54 |
members( 1, 2 ); |
55 |
} |
56 |
bond[2]{ |
57 |
members( 2, 3 ); |
58 |
} |
59 |
bond[3]{ |
60 |
members( 3, 4 ); |
61 |
} |
62 |
bond[4]{ |
63 |
members( 4, 5 ); |
64 |
} |
65 |
bond[5]{ |
66 |
members( 5, 6 ); |
67 |
} |
68 |
bond[6]{ |
69 |
members( 6, 7 ); |
70 |
} |
71 |
bond[7]{ |
72 |
members( 7, 8 ); |
73 |
} |
74 |
bond[8]{ |
75 |
members( 8, 9 ); |
76 |
} |
77 |
|
78 |
nBends = 9; |
79 |
|
80 |
bend[0]{ |
81 |
members( 0, 1, 2 ); |
82 |
} |
83 |
bend[1]{ |
84 |
members( 1, 2, 3 ); |
85 |
} |
86 |
bend[2]{ |
87 |
members( 2, 3, 4 ); |
88 |
} |
89 |
bend[3]{ |
90 |
members( 3, 4, 5 ); |
91 |
} |
92 |
bend[4]{ |
93 |
members( 4, 5, 6 ); |
94 |
} |
95 |
bend[5]{ |
96 |
members( 5, 6, 7 ); |
97 |
} |
98 |
bend[6]{ |
99 |
members( 6, 7, 8 ); |
100 |
} |
101 |
bend[7]{ |
102 |
members( 7, 8, 9 ); |
103 |
} |
104 |
bend[8]{ |
105 |
members( 0, 1 ); |
106 |
ghostVectorSource = 0; |
107 |
} |
108 |
|
109 |
|
110 |
nTorsions = 7; |
111 |
|
112 |
torsion[0]{ |
113 |
members( 0, 1, 2, 3 ); |
114 |
} |
115 |
torsion[1]{ |
116 |
members( 1, 2, 3, 4 ); |
117 |
} |
118 |
torsion[2]{ |
119 |
members( 2, 3, 4, 5 ); |
120 |
} |
121 |
torsion[3]{ |
122 |
members( 3, 4, 5, 6 ); |
123 |
} |
124 |
torsion[4]{ |
125 |
members( 4, 5, 6, 7 ); |
126 |
} |
127 |
torsion[5]{ |
128 |
members( 5, 6, 7, 8 ); |
129 |
} |
130 |
torsion[6]{ |
131 |
members( 6, 7, 8, 9 ); |
132 |
} |
133 |
|
134 |
} |
135 |
|
136 |
molecule{ |
137 |
|
138 |
name = "beadLipid_2G"; |
139 |
nAtoms = 10; |
140 |
|
141 |
atom[0]{ |
142 |
type = "HEAD"; |
143 |
position( -1.743, 0.0, 2.684 ); |
144 |
orientation( 180.0, 90.0, 0.0 ); |
145 |
} |
146 |
atom[1]{ |
147 |
type = "TB2"; |
148 |
position( 0.0, 0.0, 0.0 ); |
149 |
} |
150 |
atom[2]{ |
151 |
type = "TB2"; |
152 |
position( -1.274, 0.0, -1.963 ); |
153 |
} |
154 |
atom[3]{ |
155 |
type = "TB2"; |
156 |
position( 0.0, 0.0, -3.926 ); |
157 |
} |
158 |
atom[4]{ |
159 |
type = "TB2"; |
160 |
position( -1.274, 0.0, -5.889 ); |
161 |
} |
162 |
atom[5]{ |
163 |
type = "TB2"; |
164 |
position( 0.0, 0.0, -7.852 ); |
165 |
} |
166 |
atom[6]{ |
167 |
type = "TB2"; |
168 |
position( -1.274, 0.0, -9.815 ); |
169 |
} |
170 |
atom[7]{ |
171 |
type = "TB2"; |
172 |
position( 0.0, 0.0, -11.778 ); |
173 |
} |
174 |
atom[8]{ |
175 |
type = "TB2"; |
176 |
position( -1.274, 0.0, -13.741 ); |
177 |
} |
178 |
atom[9]{ |
179 |
type = "TE2"; |
180 |
position( 0.0, 0.0, -15.704 ); |
181 |
} |
182 |
|
183 |
nBonds = 9; |
184 |
|
185 |
bond[0]{ |
186 |
members( 0, 1 ); |
187 |
} |
188 |
bond[1]{ |
189 |
members( 1, 2 ); |
190 |
} |
191 |
bond[2]{ |
192 |
members( 2, 3 ); |
193 |
} |
194 |
bond[3]{ |
195 |
members( 3, 4 ); |
196 |
} |
197 |
bond[4]{ |
198 |
members( 4, 5 ); |
199 |
} |
200 |
bond[5]{ |
201 |
members( 5, 6 ); |
202 |
} |
203 |
bond[6]{ |
204 |
members( 6, 7 ); |
205 |
} |
206 |
bond[7]{ |
207 |
members( 7, 8 ); |
208 |
} |
209 |
bond[8]{ |
210 |
members( 8, 9 ); |
211 |
} |
212 |
|
213 |
nBends = 9; |
214 |
|
215 |
bend[0]{ |
216 |
members( 0, 1, 2 ); |
217 |
} |
218 |
bend[1]{ |
219 |
members( 1, 2, 3 ); |
220 |
} |
221 |
bend[2]{ |
222 |
members( 2, 3, 4 ); |
223 |
} |
224 |
bend[3]{ |
225 |
members( 3, 4, 5 ); |
226 |
} |
227 |
bend[4]{ |
228 |
members( 4, 5, 6 ); |
229 |
} |
230 |
bend[5]{ |
231 |
members( 5, 6, 7 ); |
232 |
} |
233 |
bend[6]{ |
234 |
members( 6, 7, 8 ); |
235 |
} |
236 |
bend[7]{ |
237 |
members( 7, 8, 9 ); |
238 |
} |
239 |
bend[8]{ |
240 |
members( 0, 1 ); |
241 |
ghostVectorSource = 0; |
242 |
} |
243 |
|
244 |
|
245 |
nTorsions = 7; |
246 |
|
247 |
torsion[0]{ |
248 |
members( 0, 1, 2, 3 ); |
249 |
} |
250 |
torsion[1]{ |
251 |
members( 1, 2, 3, 4 ); |
252 |
} |
253 |
torsion[2]{ |
254 |
members( 2, 3, 4, 5 ); |
255 |
} |
256 |
torsion[3]{ |
257 |
members( 3, 4, 5, 6 ); |
258 |
} |
259 |
torsion[4]{ |
260 |
members( 4, 5, 6, 7 ); |
261 |
} |
262 |
torsion[5]{ |
263 |
members( 5, 6, 7, 8 ); |
264 |
} |
265 |
torsion[6]{ |
266 |
members( 6, 7, 8, 9 ); |
267 |
} |
268 |
|
269 |
} |
270 |
|
271 |
molecule{ |
272 |
|
273 |
name = "beadLipid_3G"; |
274 |
nAtoms = 10; |
275 |
|
276 |
atom[0]{ |
277 |
type = "HEAD"; |
278 |
position( -1.977, 0.0, 3.044 ); |
279 |
orientation( 180.0, 90.0, 0.0 ); |
280 |
} |
281 |
atom[1]{ |
282 |
type = "TB3"; |
283 |
position( 0.0, 0.0, 0.0 ); |
284 |
} |
285 |
atom[2]{ |
286 |
type = "TB3"; |
287 |
position( -1.699, 0.0, -2.617 ); |
288 |
} |
289 |
atom[3]{ |
290 |
type = "TB3"; |
291 |
position( 0.0, 0.0, -5.234 ); |
292 |
} |
293 |
atom[4]{ |
294 |
type = "TB3"; |
295 |
position( -1.699, 0.0, -7.851 ); |
296 |
} |
297 |
atom[5]{ |
298 |
type = "TB3"; |
299 |
position( 0.0, 0.0, -10.468 ); |
300 |
} |
301 |
atom[6]{ |
302 |
type = "TB3"; |
303 |
position( -1.699, 0.0, -13.085 ); |
304 |
} |
305 |
atom[7]{ |
306 |
type = "TB3"; |
307 |
position( 0.0, 0.0, -15.702 ); |
308 |
} |
309 |
atom[8]{ |
310 |
type = "TB3"; |
311 |
position( -1.699, 0.0, -18.319 ); |
312 |
} |
313 |
atom[9]{ |
314 |
type = "TE3"; |
315 |
position( 0.0, 0.0, -20.936 ); |
316 |
} |
317 |
|
318 |
nBonds = 9; |
319 |
|
320 |
bond[0]{ |
321 |
members( 0, 1 ); |
322 |
} |
323 |
bond[1]{ |
324 |
members( 1, 2 ); |
325 |
} |
326 |
bond[2]{ |
327 |
members( 2, 3 ); |
328 |
} |
329 |
bond[3]{ |
330 |
members( 3, 4 ); |
331 |
} |
332 |
bond[4]{ |
333 |
members( 4, 5 ); |
334 |
} |
335 |
bond[5]{ |
336 |
members( 5, 6 ); |
337 |
} |
338 |
bond[6]{ |
339 |
members( 6, 7 ); |
340 |
} |
341 |
bond[7]{ |
342 |
members( 7, 8 ); |
343 |
} |
344 |
bond[8]{ |
345 |
members( 8, 9 ); |
346 |
} |
347 |
|
348 |
nBends = 9; |
349 |
|
350 |
bend[0]{ |
351 |
members( 0, 1, 2 ); |
352 |
} |
353 |
bend[1]{ |
354 |
members( 1, 2, 3 ); |
355 |
} |
356 |
bend[2]{ |
357 |
members( 2, 3, 4 ); |
358 |
} |
359 |
bend[3]{ |
360 |
members( 3, 4, 5 ); |
361 |
} |
362 |
bend[4]{ |
363 |
members( 4, 5, 6 ); |
364 |
} |
365 |
bend[5]{ |
366 |
members( 5, 6, 7 ); |
367 |
} |
368 |
bend[6]{ |
369 |
members( 6, 7, 8 ); |
370 |
} |
371 |
bend[7]{ |
372 |
members( 7, 8, 9 ); |
373 |
} |
374 |
bend[8]{ |
375 |
members( 0, 1 ); |
376 |
ghostVectorSource = 0; |
377 |
} |
378 |
|
379 |
|
380 |
nTorsions = 7; |
381 |
|
382 |
torsion[0]{ |
383 |
members( 0, 1, 2, 3 ); |
384 |
} |
385 |
torsion[1]{ |
386 |
members( 1, 2, 3, 4 ); |
387 |
} |
388 |
torsion[2]{ |
389 |
members( 2, 3, 4, 5 ); |
390 |
} |
391 |
torsion[3]{ |
392 |
members( 3, 4, 5, 6 ); |
393 |
} |
394 |
torsion[4]{ |
395 |
members( 4, 5, 6, 7 ); |
396 |
} |
397 |
torsion[5]{ |
398 |
members( 5, 6, 7, 8 ); |
399 |
} |
400 |
torsion[6]{ |
401 |
members( 6, 7, 8, 9 ); |
402 |
} |
403 |
|
404 |
} |
405 |
|