samples/RNEMD/thiols.md

#ifndef __ALKANES_MD__
#define __ALKANES_MD__

molecule{
  name = "S";
  
  atom[0]{
    type = "S";
    position( 0.0, 0.0, 0.0 );
  }
}
 
molecule{

  name = "Butanethiol";
  
  
  atom[0]{
    type = "S";
    position( -0.626, 1.709, 0.0 );
  }

  atom[1]{
    type = "CH2";
    position( 0.0, 0.0, 0.0 );
  }

  atom[2]{
    type = "CH2";
    position( 1.54, 0.0, 0.0 );
  }

  atom[3]{
    type = "CH2";
    position( 2.166, -1.407, 0.0 );
  }

  atom[4]{
    type = "CH3";
    position( 3.706, -1.407, 0.0 );
  }
  

  bond{
    members( 0, 1 );
  }

  bond{
    members( 1, 2 );
  }

  bond{
    members( 2, 3 );
  }

  bond{
    members( 3, 4 );
  }

  
  bend{
    members( 0, 1, 2 );
  }

  bend{
    members( 1, 2, 3 );
  }

  bend{
    members( 2, 3, 4 );
  }

  
  torsion{
    members( 0, 1, 2, 3 );
  }

  torsion{
    members( 1, 2, 3, 4 );
  }
   
}


molecule{

  name = "Hexanethiol";
  
  
  atom[0]{
    type = "S";
    position( -0.626, 1.709, 0.0 );
  }

  atom[1]{
    type = "CH2";
    position( 0.0, 0.0, 0.0 );
  }

  atom[2]{
    type = "CH2";
    position( 1.54, 0.0, 0.0 );
  }

  atom[3]{
    type = "CH2";
    position( 2.166, -1.407, 0.0 );
  }

  atom[4]{
    type = "CH2";
    position( 3.706, -1.407, 0.0 );
  }

  atom[5]{
    type = "CH2";
    position( 4.332, -2.814, 0.0 );
  }

  atom[6]{
    type = "CH3";
    position( 5.872, -2.814, 0.0 );
  }
  

  bond{
    members( 0, 1 );
  }

  bond{
    members( 1, 2 );
  }

  bond{
    members( 2, 3 );
  }

  bond{
    members( 3, 4 );
  }

  bond{
    members( 4, 5 );
  }

  bond{
    members( 5, 6 );
  }

  
  bend{
    members( 0, 1, 2 );
  }

  bend{
    members( 1, 2, 3 );
  }

  bend{
    members( 2, 3, 4 );
  }

  bend{
    members( 3, 4, 5 );
  }

  bend{
    members( 4, 5, 6 );
  }

  
  torsion{
    members( 0, 1, 2, 3 );
  }

  torsion{
    members( 1, 2, 3, 4 );
  }

  torsion{
    members( 2, 3, 4, 5 );
  }

  torsion{
    members( 3, 4, 5, 6 );
  }
   
}


molecule{

  name = "Octanethiol";
  
  
  atom[0]{
    type = "S";
    position( -0.626, 1.709, 0.0 );
  }

  atom[1]{
    type = "CH2";
    position( 0.0, 0.0, 0.0 );
  }

  atom[2]{
    type = "CH2";
    position( 1.54, 0.0, 0.0 );
  }

  atom[3]{
    type = "CH2";
    position( 2.166, -1.407, 0.0 );
  }

  atom[4]{
    type = "CH2";
    position( 3.706, -1.407, 0.0 );
  }

  atom[5]{
    type = "CH2";
    position( 4.332, -2.814, 0.0 );
  }

  atom[6]{
    type = "CH2";
    position( 5.872, -2.814, 0.0 );
  }
  
  atom[7]{
    type = "CH2";
    position( 6.498, -4.221, 0.0 );
  }

  atom[8]{
    type = "CH3";
    position( 8.038, -4.221, 0.0 );
  }


  bond{
    members( 0, 1 );
  }

  bond{
    members( 1, 2 );
  }

  bond{
    members( 2, 3 );
  }

  bond{
    members( 3, 4 );
  }

  bond{
    members( 4, 5 );
  }

  bond{
    members( 5, 6 );
  }

  bond{
    members( 6, 7 );
  }

  bond{
    members( 7, 8 );
  }

  
  bend{
    members( 0, 1, 2 );
  }

  bend{
    members( 1, 2, 3 );
  }

  bend{
    members( 2, 3, 4 );
  }

  bend{
    members( 3, 4, 5 );
  }

  bend{
    members( 4, 5, 6 );
  }

  bend{
    members( 5, 6, 7 );
  }

  bend{
    members( 6, 7, 8 );
  }

  
  torsion{
    members( 0, 1, 2, 3 );
  }

  torsion{
    members( 1, 2, 3, 4 );
  }

  torsion{
    members( 2, 3, 4, 5 );
  }

  torsion{
    members( 3, 4, 5, 6 );
  }

  torsion{
    members( 4, 5, 6, 7 );
  }

  torsion{
    members( 5, 6, 7, 8 );
  }
   
}


molecule{

  name = "Decanethiol";
  
  
  atom[0]{
    type = "S";
    position( -0.626, 1.709, 0.0 );
  }

  atom[1]{
    type = "CH2";
    position( 0.0, 0.0, 0.0 );
  }

  atom[2]{
    type = "CH2";
    position( 1.54, 0.0, 0.0 );
  }

  atom[3]{
    type = "CH2";
    position( 2.166, -1.407, 0.0 );
  }

  atom[4]{
    type = "CH2";
    position( 3.706, -1.407, 0.0 );
  }

  atom[5]{
    type = "CH2";
    position( 4.332, -2.814, 0.0 );
  }

  atom[6]{
    type = "CH2";
    position( 5.872, -2.814, 0.0 );
  }
  
  atom[7]{
    type = "CH2";
    position( 6.498, -4.221, 0.0 );
  }

  atom[8]{
    type = "CH2";
    position( 8.038, -4.221, 0.0 );
  }

  atom[9]{
    type = "CH2";
    position( 8.664, -5.628, 0.0 );
  }

  atom[10]{
    type = "CH3";
    position( 10.204, -5.628, 0.0 );
  }


  bond{
    members( 0, 1 );
  }

  bond{
    members( 1, 2 );
  }

  bond{
    members( 2, 3 );
  }

  bond{
    members( 3, 4 );
  }

  bond{
    members( 4, 5 );
  }

  bond{
    members( 5, 6 );
  }

  bond{
    members( 6, 7 );
  }

  bond{
    members( 7, 8 );
  }

  bond{
    members( 8, 9 );
  }

  bond{
    members( 9, 10 );
  }

  
  bend{
    members( 0, 1, 2 );
  }

  bend{
    members( 1, 2, 3 );
  }

  bend{
    members( 2, 3, 4 );
  }

  bend{
    members( 3, 4, 5 );
  }

  bend{
    members( 4, 5, 6 );
  }

  bend{
    members( 5, 6, 7 );
  }

  bend{
    members( 6, 7, 8 );
  }

  bend{
    members( 7, 8, 9 );
  }

  bend{
    members( 8, 9, 10 );
  }

  
  torsion{
    members( 0, 1, 2, 3 );
  }

  torsion{
    members( 1, 2, 3, 4 );
  }

  torsion{
    members( 2, 3, 4, 5 );
  }

  torsion{
    members( 3, 4, 5, 6 );
  }

  torsion{
    members( 4, 5, 6, 7 );
  }

  torsion{
    members( 5, 6, 7, 8 );
  }

  torsion{
    members( 6, 7, 8, 9 );
  }

  torsion{
    members( 7, 8, 9, 10 );
  }
   
}


molecule{

  name = "Dodecanethiol";
  
  
  atom[0]{
    type = "S";
    position( -0.626, 1.709, 0.0 );
  }

  atom[1]{
    type = "CH2";
    position( 0.0, 0.0, 0.0 );
  }

  atom[2]{
    type = "CH2";
    position( 1.54, 0.0, 0.0 );
  }

  atom[3]{
    type = "CH2";
    position( 2.166, -1.407, 0.0 );
  }

  atom[4]{
    type = "CH2";
    position( 3.706, -1.407, 0.0 );
  }

  atom[5]{
    type = "CH2";
    position( 4.332, -2.814, 0.0 );
  }

  atom[6]{
    type = "CH2";
    position( 5.872, -2.814, 0.0 );
  }
  
  atom[7]{
    type = "CH2";
    position( 6.498, -4.221, 0.0 );
  }

  atom[8]{
    type = "CH2";
    position( 8.038, -4.221, 0.0 );
  }

  atom[9]{
    type = "CH2";
    position( 8.664, -5.628, 0.0 );
  }

  atom[10]{
    type = "CH2";
    position( 10.204, -5.628, 0.0 );
  }

  atom[11]{
    type = "CH2";
    position( 10.830, -7.035, 0.0 );
  }

  atom[12]{
    type = "CH3";
    position( 12.370, -7.035, 0.0 );
  }


  bond{
    members( 0, 1 );
  }

  bond{
    members( 1, 2 );
  }

  bond{
    members( 2, 3 );
  }

  bond{
    members( 3, 4 );
  }

  bond{
    members( 4, 5 );
  }

  bond{
    members( 5, 6 );
  }

  bond{
    members( 6, 7 );
  }

  bond{
    members( 7, 8 );
  }

  bond{
    members( 8, 9 );
  }

  bond{
    members( 9, 10 );
  }

  bond{
    members( 10, 11 );
  }

  bond{
    members( 11, 12 );
  }
  

  bend{
    members( 0, 1, 2 );
  }

  bend{
    members( 1, 2, 3 );
  }

  bend{
    members( 2, 3, 4 );
  }

  bend{
    members( 3, 4, 5 );
  }

  bend{
    members( 4, 5, 6 );
  }

  bend{
    members( 5, 6, 7 );
  }

  bend{
    members( 6, 7, 8 );
  }

  bend{
    members( 7, 8, 9 );
  }

  bend{
    members( 8, 9, 10 );
  }

  bend{
    members( 9, 10, 11 );
  }

  bend{
    members( 10, 11, 12 );
  }

  
  torsion{
    members( 0, 1, 2, 3 );
  }

  torsion{
    members( 1, 2, 3, 4 );
  }

  torsion{
    members( 2, 3, 4, 5 );
  }

  torsion{
    members( 3, 4, 5, 6 );
  }

  torsion{
    members( 4, 5, 6, 7 );
  }

  torsion{
    members( 5, 6, 7, 8 );
  }

  torsion{
    members( 6, 7, 8, 9 );
  }

  torsion{
    members( 7, 8, 9, 10 );
  }

  torsion{
    members( 8, 9, 10, 11 );
  }

  torsion{
    members( 9, 10, 11, 12 );
  }
   
}

#endif
Revision:	1783
Committed:	Wed Aug 22 17:20:40 2012 UTC (12 years, 9 months ago) by kstocke1
File size:	7501 byte(s)
Log Message:	Added 6, 8, 10 and 12 length alkane chains to thiols
#	Content
1	#ifndef __ALKANES_MD__
2	#define __ALKANES_MD__
3
4	molecule{
5	name = "S";
6
7	atom[0]{
8	type = "S";
9	position( 0.0, 0.0, 0.0 );
10	}
11	}
12
13	molecule{
14
15	name = "Butanethiol";
16
17
18	atom[0]{
19	type = "S";
20	position( -0.626, 1.709, 0.0 );
21	}
22
23	atom[1]{
24	type = "CH2";
25	position( 0.0, 0.0, 0.0 );
26	}
27
28	atom[2]{
29	type = "CH2";
30	position( 1.54, 0.0, 0.0 );
31	}
32
33	atom[3]{
34	type = "CH2";
35	position( 2.166, -1.407, 0.0 );
36	}
37
38	atom[4]{
39	type = "CH3";
40	position( 3.706, -1.407, 0.0 );
41	}
42
43
44	bond{
45	members( 0, 1 );
46	}
47
48	bond{
49	members( 1, 2 );
50	}
51
52	bond{
53	members( 2, 3 );
54	}
55
56	bond{
57	members( 3, 4 );
58	}
59
60
61	bend{
62	members( 0, 1, 2 );
63	}
64
65	bend{
66	members( 1, 2, 3 );
67	}
68
69	bend{
70	members( 2, 3, 4 );
71	}
72
73
74	torsion{
75	members( 0, 1, 2, 3 );
76	}
77
78	torsion{
79	members( 1, 2, 3, 4 );
80	}
81
82	}
83
84
85	molecule{
86
87	name = "Hexanethiol";
88
89
90	atom[0]{
91	type = "S";
92	position( -0.626, 1.709, 0.0 );
93	}
94
95	atom[1]{
96	type = "CH2";
97	position( 0.0, 0.0, 0.0 );
98	}
99
100	atom[2]{
101	type = "CH2";
102	position( 1.54, 0.0, 0.0 );
103	}
104
105	atom[3]{
106	type = "CH2";
107	position( 2.166, -1.407, 0.0 );
108	}
109
110	atom[4]{
111	type = "CH2";
112	position( 3.706, -1.407, 0.0 );
113	}
114
115	atom[5]{
116	type = "CH2";
117	position( 4.332, -2.814, 0.0 );
118	}
119
120	atom[6]{
121	type = "CH3";
122	position( 5.872, -2.814, 0.0 );
123	}
124
125
126	bond{
127	members( 0, 1 );
128	}
129
130	bond{
131	members( 1, 2 );
132	}
133
134	bond{
135	members( 2, 3 );
136	}
137
138	bond{
139	members( 3, 4 );
140	}
141
142	bond{
143	members( 4, 5 );
144	}
145
146	bond{
147	members( 5, 6 );
148	}
149
150
151	bend{
152	members( 0, 1, 2 );
153	}
154
155	bend{
156	members( 1, 2, 3 );
157	}
158
159	bend{
160	members( 2, 3, 4 );
161	}
162
163	bend{
164	members( 3, 4, 5 );
165	}
166
167	bend{
168	members( 4, 5, 6 );
169	}
170
171
172	torsion{
173	members( 0, 1, 2, 3 );
174	}
175
176	torsion{
177	members( 1, 2, 3, 4 );
178	}
179
180	torsion{
181	members( 2, 3, 4, 5 );
182	}
183
184	torsion{
185	members( 3, 4, 5, 6 );
186	}
187
188	}
189
190
191	molecule{
192
193	name = "Octanethiol";
194
195
196	atom[0]{
197	type = "S";
198	position( -0.626, 1.709, 0.0 );
199	}
200
201	atom[1]{
202	type = "CH2";
203	position( 0.0, 0.0, 0.0 );
204	}
205
206	atom[2]{
207	type = "CH2";
208	position( 1.54, 0.0, 0.0 );
209	}
210
211	atom[3]{
212	type = "CH2";
213	position( 2.166, -1.407, 0.0 );
214	}
215
216	atom[4]{
217	type = "CH2";
218	position( 3.706, -1.407, 0.0 );
219	}
220
221	atom[5]{
222	type = "CH2";
223	position( 4.332, -2.814, 0.0 );
224	}
225
226	atom[6]{
227	type = "CH2";
228	position( 5.872, -2.814, 0.0 );
229	}
230
231	atom[7]{
232	type = "CH2";
233	position( 6.498, -4.221, 0.0 );
234	}
235
236	atom[8]{
237	type = "CH3";
238	position( 8.038, -4.221, 0.0 );
239	}
240
241
242	bond{
243	members( 0, 1 );
244	}
245
246	bond{
247	members( 1, 2 );
248	}
249
250	bond{
251	members( 2, 3 );
252	}
253
254	bond{
255	members( 3, 4 );
256	}
257
258	bond{
259	members( 4, 5 );
260	}
261
262	bond{
263	members( 5, 6 );
264	}
265
266	bond{
267	members( 6, 7 );
268	}
269
270	bond{
271	members( 7, 8 );
272	}
273
274
275	bend{
276	members( 0, 1, 2 );
277	}
278
279	bend{
280	members( 1, 2, 3 );
281	}
282
283	bend{
284	members( 2, 3, 4 );
285	}
286
287	bend{
288	members( 3, 4, 5 );
289	}
290
291	bend{
292	members( 4, 5, 6 );
293	}
294
295	bend{
296	members( 5, 6, 7 );
297	}
298
299	bend{
300	members( 6, 7, 8 );
301	}
302
303
304	torsion{
305	members( 0, 1, 2, 3 );
306	}
307
308	torsion{
309	members( 1, 2, 3, 4 );
310	}
311
312	torsion{
313	members( 2, 3, 4, 5 );
314	}
315
316	torsion{
317	members( 3, 4, 5, 6 );
318	}
319
320	torsion{
321	members( 4, 5, 6, 7 );
322	}
323
324	torsion{
325	members( 5, 6, 7, 8 );
326	}
327
328	}
329
330
331	molecule{
332
333	name = "Decanethiol";
334
335
336	atom[0]{
337	type = "S";
338	position( -0.626, 1.709, 0.0 );
339	}
340
341	atom[1]{
342	type = "CH2";
343	position( 0.0, 0.0, 0.0 );
344	}
345
346	atom[2]{
347	type = "CH2";
348	position( 1.54, 0.0, 0.0 );
349	}
350
351	atom[3]{
352	type = "CH2";
353	position( 2.166, -1.407, 0.0 );
354	}
355
356	atom[4]{
357	type = "CH2";
358	position( 3.706, -1.407, 0.0 );
359	}
360
361	atom[5]{
362	type = "CH2";
363	position( 4.332, -2.814, 0.0 );
364	}
365
366	atom[6]{
367	type = "CH2";
368	position( 5.872, -2.814, 0.0 );
369	}
370
371	atom[7]{
372	type = "CH2";
373	position( 6.498, -4.221, 0.0 );
374	}
375
376	atom[8]{
377	type = "CH2";
378	position( 8.038, -4.221, 0.0 );
379	}
380
381	atom[9]{
382	type = "CH2";
383	position( 8.664, -5.628, 0.0 );
384	}
385
386	atom[10]{
387	type = "CH3";
388	position( 10.204, -5.628, 0.0 );
389	}
390
391
392	bond{
393	members( 0, 1 );
394	}
395
396	bond{
397	members( 1, 2 );
398	}
399
400	bond{
401	members( 2, 3 );
402	}
403
404	bond{
405	members( 3, 4 );
406	}
407
408	bond{
409	members( 4, 5 );
410	}
411
412	bond{
413	members( 5, 6 );
414	}
415
416	bond{
417	members( 6, 7 );
418	}
419
420	bond{
421	members( 7, 8 );
422	}
423
424	bond{
425	members( 8, 9 );
426	}
427
428	bond{
429	members( 9, 10 );
430	}
431
432
433	bend{
434	members( 0, 1, 2 );
435	}
436
437	bend{
438	members( 1, 2, 3 );
439	}
440
441	bend{
442	members( 2, 3, 4 );
443	}
444
445	bend{
446	members( 3, 4, 5 );
447	}
448
449	bend{
450	members( 4, 5, 6 );
451	}
452
453	bend{
454	members( 5, 6, 7 );
455	}
456
457	bend{
458	members( 6, 7, 8 );
459	}
460
461	bend{
462	members( 7, 8, 9 );
463	}
464
465	bend{
466	members( 8, 9, 10 );
467	}
468
469
470	torsion{
471	members( 0, 1, 2, 3 );
472	}
473
474	torsion{
475	members( 1, 2, 3, 4 );
476	}
477
478	torsion{
479	members( 2, 3, 4, 5 );
480	}
481
482	torsion{
483	members( 3, 4, 5, 6 );
484	}
485
486	torsion{
487	members( 4, 5, 6, 7 );
488	}
489
490	torsion{
491	members( 5, 6, 7, 8 );
492	}
493
494	torsion{
495	members( 6, 7, 8, 9 );
496	}
497
498	torsion{
499	members( 7, 8, 9, 10 );
500	}
501
502	}
503
504
505	molecule{
506
507	name = "Dodecanethiol";
508
509
510	atom[0]{
511	type = "S";
512	position( -0.626, 1.709, 0.0 );
513	}
514
515	atom[1]{
516	type = "CH2";
517	position( 0.0, 0.0, 0.0 );
518	}
519
520	atom[2]{
521	type = "CH2";
522	position( 1.54, 0.0, 0.0 );
523	}
524
525	atom[3]{
526	type = "CH2";
527	position( 2.166, -1.407, 0.0 );
528	}
529
530	atom[4]{
531	type = "CH2";
532	position( 3.706, -1.407, 0.0 );
533	}
534
535	atom[5]{
536	type = "CH2";
537	position( 4.332, -2.814, 0.0 );
538	}
539
540	atom[6]{
541	type = "CH2";
542	position( 5.872, -2.814, 0.0 );
543	}
544
545	atom[7]{
546	type = "CH2";
547	position( 6.498, -4.221, 0.0 );
548	}
549
550	atom[8]{
551	type = "CH2";
552	position( 8.038, -4.221, 0.0 );
553	}
554
555	atom[9]{
556	type = "CH2";
557	position( 8.664, -5.628, 0.0 );
558	}
559
560	atom[10]{
561	type = "CH2";
562	position( 10.204, -5.628, 0.0 );
563	}
564
565	atom[11]{
566	type = "CH2";
567	position( 10.830, -7.035, 0.0 );
568	}
569
570	atom[12]{
571	type = "CH3";
572	position( 12.370, -7.035, 0.0 );
573	}
574
575
576	bond{
577	members( 0, 1 );
578	}
579
580	bond{
581	members( 1, 2 );
582	}
583
584	bond{
585	members( 2, 3 );
586	}
587
588	bond{
589	members( 3, 4 );
590	}
591
592	bond{
593	members( 4, 5 );
594	}
595
596	bond{
597	members( 5, 6 );
598	}
599
600	bond{
601	members( 6, 7 );
602	}
603
604	bond{
605	members( 7, 8 );
606	}
607
608	bond{
609	members( 8, 9 );
610	}
611
612	bond{
613	members( 9, 10 );
614	}
615
616	bond{
617	members( 10, 11 );
618	}
619
620	bond{
621	members( 11, 12 );
622	}
623
624
625	bend{
626	members( 0, 1, 2 );
627	}
628
629	bend{
630	members( 1, 2, 3 );
631	}
632
633	bend{
634	members( 2, 3, 4 );
635	}
636
637	bend{
638	members( 3, 4, 5 );
639	}
640
641	bend{
642	members( 4, 5, 6 );
643	}
644
645	bend{
646	members( 5, 6, 7 );
647	}
648
649	bend{
650	members( 6, 7, 8 );
651	}
652
653	bend{
654	members( 7, 8, 9 );
655	}
656
657	bend{
658	members( 8, 9, 10 );
659	}
660
661	bend{
662	members( 9, 10, 11 );
663	}
664
665	bend{
666	members( 10, 11, 12 );
667	}
668
669
670	torsion{
671	members( 0, 1, 2, 3 );
672	}
673
674	torsion{
675	members( 1, 2, 3, 4 );
676	}
677
678	torsion{
679	members( 2, 3, 4, 5 );
680	}
681
682	torsion{
683	members( 3, 4, 5, 6 );
684	}
685
686	torsion{
687	members( 4, 5, 6, 7 );
688	}
689
690	torsion{
691	members( 5, 6, 7, 8 );
692	}
693
694	torsion{
695	members( 6, 7, 8, 9 );
696	}
697
698	torsion{
699	members( 7, 8, 9, 10 );
700	}
701
702	torsion{
703	members( 8, 9, 10, 11 );
704	}
705
706	torsion{
707	members( 9, 10, 11, 12 );
708	}
709
710	}
711
712	#endif