samples/minimizer/water.md

molecule{
  name = "SSD_E";
  nAtoms = 1;
  atom[0]{
    type = "SSD_E";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
}

molecule{
  name = "SSD_RF";
  nAtoms = 1;
  atom[0]{
    type = "SSD_RF";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
}

molecule{
  name = "SSD";
  nAtoms = 1;
  atom[0]{
    type = "SSD";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
}

molecule{
  name = "SSD1";
  nAtoms = 1;
  atom[0]{
    type = "SSD1";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
}

molecule{
  name = "TIP3P";
  nAtoms = 3;
  atom[0]{
    type = "O_TIP3P";
    position( 0.0, 0.0, -0.06556 );
  }
  atom[1]{
    type = "H_TIP3P";
    position( 0.0, 0.75695, 0.52032 );
  }
  atom[2]{
    type = "H_TIP3P";
    position( 0.0, -0.75695, 0.52032 );
  }

  nRigidBodies = 1;
  rigidBody[0]{ 
    nMembers = 3;
    members(0, 1, 2);
  }

  nCutoffGroups = 1;
  cutoffGroup[0]{
    nMembers = 3;
    members(0, 1, 2);
  }

}

molecule{
  name = "TIP4P";
  nAtoms = 4;
  atom[0]{
    type = "O_TIP4P";
    position( 0.0, 0.0, -0.06556 );
  }
  atom[1]{
    type = "H_TIP4P";
    position( 0.0, 0.75695, 0.52032 );
  }
  atom[2]{
    type = "H_TIP4P";
    position( 0.0, -0.75695, 0.52032 );
  }
  atom[3]{
    type = "EP_TIP4P";
    position( 0.0, 0.0, 0.08444 );
  }
  nRigidBodies = 1;
  rigidBody[0]{
    nMembers = 4;
    members(0, 1, 2, 3);
  }

  nCutoffGroups = 1;
  cutoffGroup[0]{
    nMembers = 4;
    members(0, 1, 2, 3);
  }

}

molecule{
  name = "TIP5P";
  nAtoms = 5;
  atom[0]{
    type = "O_TIP5P";
    position( 0.0, 0.0, -0.06556 );
  }
  atom[1]{
    type = "H_TIP5P";
    position( 0.0, 0.75695, 0.52032 );
  }
  atom[2]{
    type = "H_TIP5P";
    position( 0.0, -0.75695, 0.52032 );
  }
  atom[3]{
    type = "EP_TIP5P";
    position( 0.57154, 0.0, -0.46971 );
  }
  atom[4]{
    type = "EP_TIP5P";
    position( -0.57154, 0.0, -0.46971 );
  }
  nRigidBodies = 1;
  rigidBody[0]{
    nMembers = 5;
    members(0, 1, 2, 3, 4);
  }

  nCutoffGroups = 1;
  cutoffGroup[0]{
    nMembers = 5;
    members(0, 1, 2, 3, 4);
  }

}

molecule{
  name = "SPCE";
  nAtoms = 3;
  atom[0]{
    type = "O_SPCE";
    position( 0.0, 0.0, -0.06461 );
  }
  atom[1]{
    type = "H_SPCE";
    position( 0.0, 0.81649, 0.51275 );
  }
  atom[2]{
    type = "H_SPCE";
    position( 0.0, -0.81649, 0.51275 );
  }
  nRigidBodies = 1;
  rigidBody[0]{
    nMembers = 3;
    members(0, 1, 2);
  }

  nCutoffGroups = 1;
  cutoffGroup[0]{
    nMembers = 3;
    members(0, 1, 2);
  }

}

molecule{
  name = "DPD";
  nAtoms = 1;
  atom[0]{
    type = "DPD";
    position(0.0, 0.0, 0.0);
  }
}

molecule{
  name = "OFAKE";
  nAtoms = 1;
  atom[0]{
    type = "O_TIP3P";
    position( 0.0, 0.0, -0.06556 );
  }
}

molecule{
  name = "HFAKE";
  nAtoms = 1;
  atom[0]{
    type = "H_FAKE";
    position( 0.0, 0.0, -0.06556 );
  }
}


Revision:	1490
Committed:	Fri Sep 24 04:16:43 2004 UTC (19 years, 9 months ago) by gezelter
File size:	2907 byte(s)
Log Message:	Import of OOPSE v. 2.0
#	User	Rev	Content
1	gezelter	1490	molecule{
2			name = "SSD_E";
3			nAtoms = 1;
4			atom[0]{
5			type = "SSD_E";
6			position( 0.0, 0.0, 0.0 );
7			orientation( 0.0, 0.0, 0.0 );
8			}
9			}
10
11			molecule{
12			name = "SSD_RF";
13			nAtoms = 1;
14			atom[0]{
15			type = "SSD_RF";
16			position( 0.0, 0.0, 0.0 );
17			orientation( 0.0, 0.0, 0.0 );
18			}
19			}
20
21			molecule{
22			name = "SSD";
23			nAtoms = 1;
24			atom[0]{
25			type = "SSD";
26			position( 0.0, 0.0, 0.0 );
27			orientation( 0.0, 0.0, 0.0 );
28			}
29			}
30
31			molecule{
32			name = "SSD1";
33			nAtoms = 1;
34			atom[0]{
35			type = "SSD1";
36			position( 0.0, 0.0, 0.0 );
37			orientation( 0.0, 0.0, 0.0 );
38			}
39			}
40
41			molecule{
42			name = "TIP3P";
43			nAtoms = 3;
44			atom[0]{
45			type = "O_TIP3P";
46			position( 0.0, 0.0, -0.06556 );
47			}
48			atom[1]{
49			type = "H_TIP3P";
50			position( 0.0, 0.75695, 0.52032 );
51			}
52			atom[2]{
53			type = "H_TIP3P";
54			position( 0.0, -0.75695, 0.52032 );
55			}
56
57			nRigidBodies = 1;
58			rigidBody[0]{
59			nMembers = 3;
60			members(0, 1, 2);
61			}
62
63			nCutoffGroups = 1;
64			cutoffGroup[0]{
65			nMembers = 3;
66			members(0, 1, 2);
67			}
68
69			}
70
71			molecule{
72			name = "TIP4P";
73			nAtoms = 4;
74			atom[0]{
75			type = "O_TIP4P";
76			position( 0.0, 0.0, -0.06556 );
77			}
78			atom[1]{
79			type = "H_TIP4P";
80			position( 0.0, 0.75695, 0.52032 );
81			}
82			atom[2]{
83			type = "H_TIP4P";
84			position( 0.0, -0.75695, 0.52032 );
85			}
86			atom[3]{
87			type = "EP_TIP4P";
88			position( 0.0, 0.0, 0.08444 );
89			}
90			nRigidBodies = 1;
91			rigidBody[0]{
92			nMembers = 4;
93			members(0, 1, 2, 3);
94			}
95
96			nCutoffGroups = 1;
97			cutoffGroup[0]{
98			nMembers = 4;
99			members(0, 1, 2, 3);
100			}
101
102			}
103
104			molecule{
105			name = "TIP5P";
106			nAtoms = 5;
107			atom[0]{
108			type = "O_TIP5P";
109			position( 0.0, 0.0, -0.06556 );
110			}
111			atom[1]{
112			type = "H_TIP5P";
113			position( 0.0, 0.75695, 0.52032 );
114			}
115			atom[2]{
116			type = "H_TIP5P";
117			position( 0.0, -0.75695, 0.52032 );
118			}
119			atom[3]{
120			type = "EP_TIP5P";
121			position( 0.57154, 0.0, -0.46971 );
122			}
123			atom[4]{
124			type = "EP_TIP5P";
125			position( -0.57154, 0.0, -0.46971 );
126			}
127			nRigidBodies = 1;
128			rigidBody[0]{
129			nMembers = 5;
130			members(0, 1, 2, 3, 4);
131			}
132
133			nCutoffGroups = 1;
134			cutoffGroup[0]{
135			nMembers = 5;
136			members(0, 1, 2, 3, 4);
137			}
138
139			}
140
141			molecule{
142			name = "SPCE";
143			nAtoms = 3;
144			atom[0]{
145			type = "O_SPCE";
146			position( 0.0, 0.0, -0.06461 );
147			}
148			atom[1]{
149			type = "H_SPCE";
150			position( 0.0, 0.81649, 0.51275 );
151			}
152			atom[2]{
153			type = "H_SPCE";
154			position( 0.0, -0.81649, 0.51275 );
155			}
156			nRigidBodies = 1;
157			rigidBody[0]{
158			nMembers = 3;
159			members(0, 1, 2);
160			}
161
162			nCutoffGroups = 1;
163			cutoffGroup[0]{
164			nMembers = 3;
165			members(0, 1, 2);
166			}
167
168			}
169
170			molecule{
171			name = "DPD";
172			nAtoms = 1;
173			atom[0]{
174			type = "DPD";
175			position(0.0, 0.0, 0.0);
176			}
177			}
178
179			molecule{
180			name = "OFAKE";
181			nAtoms = 1;
182			atom[0]{
183			type = "O_TIP3P";
184			position( 0.0, 0.0, -0.06556 );
185			}
186			}
187
188			molecule{
189			name = "HFAKE";
190			nAtoms = 1;
191			atom[0]{
192			type = "H_FAKE";
193			position( 0.0, 0.0, -0.06556 );
194			}
195			}
196
197