metals/minimizer/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 );
  }
   
}

#endif
Revision:	1257
Committed:	Wed Jun 11 16:49:56 2008 UTC (17 years, 5 months ago) by chuckv
File size:	879 byte(s)
Log Message:	Code work on thiols and TraPPE torsions.
#	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
45
46	bond{
47	members( 0, 1 );
48	}
49
50	bond{
51	members( 1, 2 );
52	}
53
54	bond{
55	members( 2, 3 );
56	}
57
58	bond{
59	members( 3, 4 );
60	}
61
62
63	bend{
64	members( 0, 1, 2 );
65	}
66
67	bend{
68	members( 1, 2, 3 );
69	}
70
71	bend{
72	members( 2, 3, 4 );
73	}
74
75
76	torsion{
77	members( 0, 1, 2, 3 );
78	}
79
80	torsion{
81	members( 1, 2, 3, 4 );
82	}
83
84	}
85
86	#endif