samples/minimizer/water.md

#ifndef _WATER_MD_
#define _WATER_MD_

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

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

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

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

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

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

molecule{
  name = "TRED";
  
  atom[0]{
    type = "TRED";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
  atom[1]{
    type = "EP_TRED";
    position( 0.0, 0.0, 0.5 );
  }

  rigidBody[0]{
    members(0, 1);
  }
}

molecule{
  name = "TIP3P";
  
  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 );
  }
  
  rigidBody[0]{     
    members(0, 1, 2);
  }  
}

molecule{
  name = "TIP4P";
  
  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 );
  }
  
  rigidBody[0]{    
    members(0, 1, 2, 3);
  }  
}

molecule{
  name = "TIP4P-Ew";
  
  atom[0]{
    type = "O_TIP4P-Ew";
    position( 0.0, 0.0, -0.06556 );
  }
  atom[1]{
    type = "H_TIP4P-Ew";
    position( 0.0, 0.75695, 0.52032 );
  }
  atom[2]{
    type = "H_TIP4P-Ew";
    position( 0.0, -0.75695, 0.52032 );
  }
  atom[3]{
    type = "EP_TIP4P-Ew";
    position( 0.0, 0.0, 0.05944 );
  }
  
  rigidBody[0]{    
    members(0, 1, 2, 3);
  }
}

molecule{
  name = "TIP5P";
  
  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 );
  }
  
  rigidBody[0]{
    members(0, 1, 2, 3, 4);
  }
}

molecule{
  name = "TIP5P-E";
  
  atom[0]{
    type = "O_TIP5P-E";
    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 );
  }
  
  rigidBody[0]{    
    members(0, 1, 2, 3, 4);
  }
}

molecule{
  name = "SPCE";
  
  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 );
  }
  
  rigidBody[0]{    
    members(0, 1, 2);
  }
}

molecule{
  name = "SPC";
  
  atom[0]{
    type = "O_SPC";
    position( 0.0, 0.0, -0.06461 );
  }
  atom[1]{
    type = "H_SPC";
    position( 0.0, 0.81649, 0.51275 );
  }
  atom[2]{
    type = "H_SPC";
    position( 0.0, -0.81649, 0.51275 );
  }
  
  rigidBody[0]{    
    members(0, 1, 2);
  }
}

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

#endif
Revision:	1393
Committed:	Wed Nov 25 20:36:46 2009 UTC (15 years, 5 months ago) by gezelter
File size:	3749 byte(s)
Log Message:	removing spurious cutoffGroup lines from default water.md sample files
#	User	Rev	Content
1	gezelter	1393	#ifndef _WATER_MD_
2			#define _WATER_MD_
3
4	gezelter	2	molecule{
5	gezelter	1393	name = "Cl-";
6
7			atom[0]{
8			type = "Cl-";
9			position(0.0, 0.0, 0.0);
10			}
11			}
12
13			molecule{
14			name = "Na+";
15
16			atom[0]{
17			type = "Na+";
18			position(0.0, 0.0, 0.0);
19			}
20			}
21
22			molecule{
23	gezelter	2	name = "SSD_E";
24	tim	790
25	gezelter	2	atom[0]{
26			type = "SSD_E";
27			position( 0.0, 0.0, 0.0 );
28			orientation( 0.0, 0.0, 0.0 );
29			}
30			}
31
32			molecule{
33			name = "SSD_RF";
34	tim	790
35	gezelter	2	atom[0]{
36			type = "SSD_RF";
37			position( 0.0, 0.0, 0.0 );
38			orientation( 0.0, 0.0, 0.0 );
39			}
40			}
41
42			molecule{
43			name = "SSD";
44	tim	790
45	gezelter	2	atom[0]{
46			type = "SSD";
47			position( 0.0, 0.0, 0.0 );
48			orientation( 0.0, 0.0, 0.0 );
49			}
50			}
51
52			molecule{
53			name = "SSD1";
54	tim	790
55	gezelter	2	atom[0]{
56			type = "SSD1";
57			position( 0.0, 0.0, 0.0 );
58			orientation( 0.0, 0.0, 0.0 );
59			}
60			}
61
62			molecule{
63	gezelter	1393	name = "TRED";
64
65			atom[0]{
66			type = "TRED";
67			position( 0.0, 0.0, 0.0 );
68			orientation( 0.0, 0.0, 0.0 );
69			}
70			atom[1]{
71			type = "EP_TRED";
72			position( 0.0, 0.0, 0.5 );
73			}
74
75			rigidBody[0]{
76			members(0, 1);
77			}
78			}
79
80			molecule{
81	gezelter	2	name = "TIP3P";
82	tim	790
83	gezelter	2	atom[0]{
84			type = "O_TIP3P";
85			position( 0.0, 0.0, -0.06556 );
86			}
87			atom[1]{
88			type = "H_TIP3P";
89			position( 0.0, 0.75695, 0.52032 );
90			}
91			atom[2]{
92			type = "H_TIP3P";
93			position( 0.0, -0.75695, 0.52032 );
94			}
95	tim	790
96	gezelter	1393	rigidBody[0]{
97	gezelter	2	members(0, 1, 2);
98	gezelter	1393	}
99	gezelter	2	}
100
101			molecule{
102			name = "TIP4P";
103	tim	790
104	gezelter	2	atom[0]{
105			type = "O_TIP4P";
106			position( 0.0, 0.0, -0.06556 );
107			}
108			atom[1]{
109			type = "H_TIP4P";
110			position( 0.0, 0.75695, 0.52032 );
111			}
112			atom[2]{
113			type = "H_TIP4P";
114			position( 0.0, -0.75695, 0.52032 );
115			}
116			atom[3]{
117			type = "EP_TIP4P";
118			position( 0.0, 0.0, 0.08444 );
119			}
120	tim	790
121	gezelter	1393	rigidBody[0]{
122	gezelter	2	members(0, 1, 2, 3);
123	gezelter	1393	}
124			}
125	gezelter	2
126	gezelter	1393	molecule{
127			name = "TIP4P-Ew";
128	tim	790
129	gezelter	1393	atom[0]{
130			type = "O_TIP4P-Ew";
131			position( 0.0, 0.0, -0.06556 );
132			}
133			atom[1]{
134			type = "H_TIP4P-Ew";
135			position( 0.0, 0.75695, 0.52032 );
136			}
137			atom[2]{
138			type = "H_TIP4P-Ew";
139			position( 0.0, -0.75695, 0.52032 );
140			}
141			atom[3]{
142			type = "EP_TIP4P-Ew";
143			position( 0.0, 0.0, 0.05944 );
144			}
145
146			rigidBody[0]{
147	gezelter	2	members(0, 1, 2, 3);
148			}
149			}
150
151			molecule{
152			name = "TIP5P";
153	tim	790
154	gezelter	2	atom[0]{
155			type = "O_TIP5P";
156			position( 0.0, 0.0, -0.06556 );
157			}
158			atom[1]{
159			type = "H_TIP5P";
160			position( 0.0, 0.75695, 0.52032 );
161			}
162			atom[2]{
163			type = "H_TIP5P";
164			position( 0.0, -0.75695, 0.52032 );
165			}
166			atom[3]{
167			type = "EP_TIP5P";
168			position( 0.57154, 0.0, -0.46971 );
169			}
170			atom[4]{
171			type = "EP_TIP5P";
172			position( -0.57154, 0.0, -0.46971 );
173			}
174	tim	790
175	gezelter	2	rigidBody[0]{
176			members(0, 1, 2, 3, 4);
177			}
178	gezelter	1393	}
179	gezelter	2
180	gezelter	1393	molecule{
181			name = "TIP5P-E";
182	tim	790
183	gezelter	1393	atom[0]{
184			type = "O_TIP5P-E";
185			position( 0.0, 0.0, -0.06556 );
186			}
187			atom[1]{
188			type = "H_TIP5P";
189			position( 0.0, 0.75695, 0.52032 );
190			}
191			atom[2]{
192			type = "H_TIP5P";
193			position( 0.0, -0.75695, 0.52032 );
194			}
195			atom[3]{
196			type = "EP_TIP5P";
197			position( 0.57154, 0.0, -0.46971 );
198			}
199			atom[4]{
200			type = "EP_TIP5P";
201			position( -0.57154, 0.0, -0.46971 );
202			}
203
204			rigidBody[0]{
205	gezelter	2	members(0, 1, 2, 3, 4);
206			}
207			}
208
209			molecule{
210			name = "SPCE";
211	tim	790
212	gezelter	2	atom[0]{
213			type = "O_SPCE";
214			position( 0.0, 0.0, -0.06461 );
215			}
216			atom[1]{
217			type = "H_SPCE";
218			position( 0.0, 0.81649, 0.51275 );
219			}
220			atom[2]{
221			type = "H_SPCE";
222			position( 0.0, -0.81649, 0.51275 );
223			}
224	tim	790
225	gezelter	1393	rigidBody[0]{
226	gezelter	2	members(0, 1, 2);
227			}
228			}
229
230			molecule{
231	gezelter	1393	name = "SPC";
232	tim	790
233	gezelter	2	atom[0]{
234	gezelter	1393	type = "O_SPC";
235			position( 0.0, 0.0, -0.06461 );
236	gezelter	2	}
237	gezelter	1393	atom[1]{
238			type = "H_SPC";
239			position( 0.0, 0.81649, 0.51275 );
240			}
241			atom[2]{
242			type = "H_SPC";
243			position( 0.0, -0.81649, 0.51275 );
244			}
245	tim	790
246	gezelter	1393	rigidBody[0]{
247			members(0, 1, 2);
248	gezelter	2	}
249			}
250
251			molecule{
252	gezelter	1393	name = "DPD";
253	tim	790
254	gezelter	2	atom[0]{
255	gezelter	1393	type = "DPD";
256			position(0.0, 0.0, 0.0);
257	gezelter	2	}
258			}
259
260	gezelter	1393	#endif