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, 8 months ago) by kstocke1
File size:	7501 byte(s)
Log Message:	Added 6, 8, 10 and 12 length alkane chains to thiols
#	User	Rev	Content
1	gezelter	1770	#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	kstocke1	1783	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	gezelter	1770
61	kstocke1	1783	bend{
62			members( 0, 1, 2 );
63			}
64	gezelter	1770
65	kstocke1	1783	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	gezelter	1770	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	kstocke1	1783	bond{
143			members( 4, 5 );
144			}
145
146			bond{
147			members( 5, 6 );
148			}
149
150	gezelter	1770
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	kstocke1	1783	bend{
164			members( 3, 4, 5 );
165			}
166
167			bend{
168			members( 4, 5, 6 );
169			}
170
171	gezelter	1770
172			torsion{
173			members( 0, 1, 2, 3 );
174			}
175
176			torsion{
177			members( 1, 2, 3, 4 );
178			}
179	kstocke1	1783
180			torsion{
181			members( 2, 3, 4, 5 );
182			}
183
184			torsion{
185			members( 3, 4, 5, 6 );
186			}
187	gezelter	1770
188			}
189
190	kstocke1	1783
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	gezelter	1770	#endif