samples/SMIPD/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:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (15 years, 4 months ago) by chuckv
File size:	879 byte(s)
Log Message:	Creating busticated version of OpenMD
#	User	Rev	Content
1	chuckv	1326	#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