samples/beadLipid/beadLipid.mdl

molecule{
  
  name = "beadLipid_1G";
  nAtoms = 10;

  atom[0]{
    type = "HEAD";
    position( -1.503, 0.0, 2.315 );
    orientation( 180.0, 90.0, 0.0 );
  }
  atom[1]{
    type = "TB1";
    position( 0.0, 0.0, 0.0 );
  }
  atom[2]{
    type = "TB1";
    position( -0.850, 0.0, -1.308 );
  }
  atom[3]{
    type = "TB1";
    position( 0.0, 0.0, -2.616 );
  }
  atom[4]{
    type = "TB1";
    position( -0.85, 0.0, -3.924 );
  }
  atom[5]{
    type = "TB1";
    position( 0.0, 0.0, -5.232 );
  }
  atom[6]{
    type = "TB1";
    position( -0.85, 0.0, -6.54 );
  }
  atom[7]{
    type = "TB1";
    position( 0.0, 0.0, -7.848 );
  }
  atom[8]{
    type = "TB1";
    position( -0.85, 0.0, -9.156 );
  }
  atom[9]{
    type = "TE1";
    position( 0.0, 0.0, -10.464 );
  }

  nBonds = 9;

  bond[0]{
    members( 0, 1 );
  }
  bond[1]{
    members( 1, 2 );
  }
  bond[2]{
    members( 2, 3 );
  }
  bond[3]{
    members( 3, 4 );
  }
  bond[4]{
    members( 4, 5 );
  }
  bond[5]{
    members( 5, 6 );
  }
  bond[6]{
    members( 6, 7 );
  }
  bond[7]{
    members( 7, 8 );
  }
  bond[8]{
    members( 8, 9 );
  }

  nBends = 9;

  bend[0]{
    members( 0, 1, 2 );
  }
  bend[1]{
    members( 1, 2, 3 );
  }
  bend[2]{
    members( 2, 3, 4 );
  }
  bend[3]{
    members( 3, 4, 5 );
  }
  bend[4]{
    members( 4, 5, 6 );
  }
  bend[5]{
    members( 5, 6, 7 );
  }
  bend[6]{
    members( 6, 7, 8 );
  }
  bend[7]{
    members( 7, 8, 9 );
  }
  bend[8]{
    members( 0, 1 );
    ghostVectorSource = 0;
  }


  nTorsions = 7;

  torsion[0]{
    members( 0, 1, 2, 3 );
  }
  torsion[1]{
    members( 1, 2, 3, 4 );
  }
  torsion[2]{
    members( 2, 3, 4, 5 );
  }
  torsion[3]{
    members( 3, 4, 5, 6 );
  }
  torsion[4]{
    members( 4, 5, 6, 7 );
  }
  torsion[5]{
    members( 5, 6, 7, 8 );
  }
  torsion[6]{
    members( 6, 7, 8, 9 );
  }

}

molecule{
  
  name = "beadLipid_2G";
  nAtoms = 10;

  atom[0]{
    type = "HEAD";
    position( -1.743, 0.0, 2.684 );
    orientation( 180.0, 90.0, 0.0 );
  }
  atom[1]{
    type = "TB2";
    position( 0.0, 0.0, 0.0 );
  }
  atom[2]{
    type = "TB2";
    position( -1.274, 0.0, -1.963 );
  }
  atom[3]{
    type = "TB2";
    position( 0.0, 0.0, -3.926 );
  }
  atom[4]{
    type = "TB2";
    position( -1.274, 0.0, -5.889 );
  }
  atom[5]{
    type = "TB2";
    position( 0.0, 0.0, -7.852 );
  }
  atom[6]{
    type = "TB2";
    position( -1.274, 0.0, -9.815 );
  }
  atom[7]{
    type = "TB2";
    position( 0.0, 0.0, -11.778 );
  }
  atom[8]{
    type = "TB2";
    position( -1.274, 0.0, -13.741 );
  }
  atom[9]{
    type = "TE2";
    position( 0.0, 0.0, -15.704 );
  }

  nBonds = 9;

  bond[0]{
    members( 0, 1 );
  }
  bond[1]{
    members( 1, 2 );
  }
  bond[2]{
    members( 2, 3 );
  }
  bond[3]{
    members( 3, 4 );
  }
  bond[4]{
    members( 4, 5 );
  }
  bond[5]{
    members( 5, 6 );
  }
  bond[6]{
    members( 6, 7 );
  }
  bond[7]{
    members( 7, 8 );
  }
  bond[8]{
    members( 8, 9 );
  }

  nBends = 9;

  bend[0]{
    members( 0, 1, 2 );
  }
  bend[1]{
    members( 1, 2, 3 );
  }
  bend[2]{
    members( 2, 3, 4 );
  }
  bend[3]{
    members( 3, 4, 5 );
  }
  bend[4]{
    members( 4, 5, 6 );
  }
  bend[5]{
    members( 5, 6, 7 );
  }
  bend[6]{
    members( 6, 7, 8 );
  }
  bend[7]{
    members( 7, 8, 9 );
  }
  bend[8]{
    members( 0, 1 );
    ghostVectorSource = 0;
  }


  nTorsions = 7;

  torsion[0]{
    members( 0, 1, 2, 3 );
  }
  torsion[1]{
    members( 1, 2, 3, 4 );
  }
  torsion[2]{
    members( 2, 3, 4, 5 );
  }
  torsion[3]{
    members( 3, 4, 5, 6 );
  }
  torsion[4]{
    members( 4, 5, 6, 7 );
  }
  torsion[5]{
    members( 5, 6, 7, 8 );
  }
  torsion[6]{
    members( 6, 7, 8, 9 );
  }

}

molecule{
  
  name = "beadLipid_3G";
  nAtoms = 10;

  atom[0]{
    type = "HEAD";
    position( -1.977, 0.0, 3.044 );
    orientation( 180.0, 90.0, 0.0 );
  }
  atom[1]{
    type = "TB3";
    position( 0.0, 0.0, 0.0 );
  }
  atom[2]{
    type = "TB3";
    position( -1.699, 0.0, -2.617 );
  }
  atom[3]{
    type = "TB3";
    position( 0.0, 0.0, -5.234 );
  }
  atom[4]{
    type = "TB3";
    position( -1.699, 0.0, -7.851 );
  }
  atom[5]{
    type = "TB3";
    position( 0.0, 0.0, -10.468 );
  }
  atom[6]{
    type = "TB3";
    position( -1.699, 0.0, -13.085 );
  }
  atom[7]{
    type = "TB3";
    position( 0.0, 0.0, -15.702 );
  }
  atom[8]{
    type = "TB3";
    position( -1.699, 0.0, -18.319 );
  }
  atom[9]{
    type = "TE3";
    position( 0.0, 0.0, -20.936 );
  }

  nBonds = 9;

  bond[0]{
    members( 0, 1 );
  }
  bond[1]{
    members( 1, 2 );
  }
  bond[2]{
    members( 2, 3 );
  }
  bond[3]{
    members( 3, 4 );
  }
  bond[4]{
    members( 4, 5 );
  }
  bond[5]{
    members( 5, 6 );
  }
  bond[6]{
    members( 6, 7 );
  }
  bond[7]{
    members( 7, 8 );
  }
  bond[8]{
    members( 8, 9 );
  }

  nBends = 9;

  bend[0]{
    members( 0, 1, 2 );
  }
  bend[1]{
    members( 1, 2, 3 );
  }
  bend[2]{
    members( 2, 3, 4 );
  }
  bend[3]{
    members( 3, 4, 5 );
  }
  bend[4]{
    members( 4, 5, 6 );
  }
  bend[5]{
    members( 5, 6, 7 );
  }
  bend[6]{
    members( 6, 7, 8 );
  }
  bend[7]{
    members( 7, 8, 9 );
  }
  bend[8]{
    members( 0, 1 );
    ghostVectorSource = 0;
  }


  nTorsions = 7;

  torsion[0]{
    members( 0, 1, 2, 3 );
  }
  torsion[1]{
    members( 1, 2, 3, 4 );
  }
  torsion[2]{
    members( 2, 3, 4, 5 );
  }
  torsion[3]{
    members( 3, 4, 5, 6 );
  }
  torsion[4]{
    members( 4, 5, 6, 7 );
  }
  torsion[5]{
    members( 5, 6, 7, 8 );
  }
  torsion[6]{
    members( 6, 7, 8, 9 );
  }

}

Revision:	985
Committed:	Mon Jan 26 21:53:35 2004 UTC (20 years, 5 months ago) by gezelter
File size:	5534 byte(s)
Log Message:	Changed orientation lines from unit vectors to euler angles
#	Content
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