water/dimer/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);
  }

  cutoffGroup{
    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);
  }

  
  cutoffGroup{
    
    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);
  }

  
  cutoffGroup{
    
    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);
  }

  
  cutoffGroup{
    
    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);
  }

  
  cutoffGroup{
    
    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);
  }

  
  cutoffGroup{
    
    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);
  }

  
  cutoffGroup{
    
    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);
  }

  
  cutoffGroup{
    
    members(0, 1, 2);
  }
}

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

#endif
Revision:	2955
Committed:	Wed Jul 19 12:46:20 2006 UTC (17 years, 11 months ago) by chrisfen
File size:	4164 byte(s)
Log Message:	Added tred to sample water.md files
#	Content
1	#ifndef _WATER_MD_
2	#define _WATER_MD_
3
4	molecule{
5	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	name = "SSD_E";
24
25	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
35	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
45	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
55	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	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	cutoffGroup{
80	members(0, 1);
81	}
82	}
83
84	molecule{
85	name = "TIP3P";
86
87	atom[0]{
88	type = "O_TIP3P";
89	position( 0.0, 0.0, -0.06556 );
90	}
91	atom[1]{
92	type = "H_TIP3P";
93	position( 0.0, 0.75695, 0.52032 );
94	}
95	atom[2]{
96	type = "H_TIP3P";
97	position( 0.0, -0.75695, 0.52032 );
98	}
99
100
101	rigidBody[0]{
102
103	members(0, 1, 2);
104	}
105
106
107	cutoffGroup{
108
109	members(0, 1, 2);
110	}
111	}
112
113	molecule{
114	name = "TIP4P";
115
116	atom[0]{
117	type = "O_TIP4P";
118	position( 0.0, 0.0, -0.06556 );
119	}
120	atom[1]{
121	type = "H_TIP4P";
122	position( 0.0, 0.75695, 0.52032 );
123	}
124	atom[2]{
125	type = "H_TIP4P";
126	position( 0.0, -0.75695, 0.52032 );
127	}
128	atom[3]{
129	type = "EP_TIP4P";
130	position( 0.0, 0.0, 0.08444 );
131	}
132
133	rigidBody[0]{
134
135	members(0, 1, 2, 3);
136	}
137
138
139	cutoffGroup{
140
141	members(0, 1, 2, 3);
142	}
143	}
144
145	molecule{
146	name = "TIP4P-Ew";
147
148	atom[0]{
149	type = "O_TIP4P-Ew";
150	position( 0.0, 0.0, -0.06556 );
151	}
152	atom[1]{
153	type = "H_TIP4P-Ew";
154	position( 0.0, 0.75695, 0.52032 );
155	}
156	atom[2]{
157	type = "H_TIP4P-Ew";
158	position( 0.0, -0.75695, 0.52032 );
159	}
160	atom[3]{
161	type = "EP_TIP4P-Ew";
162	position( 0.0, 0.0, 0.05944 );
163	}
164
165	rigidBody[0]{
166
167	members(0, 1, 2, 3);
168	}
169
170
171	cutoffGroup{
172
173	members(0, 1, 2, 3);
174	}
175	}
176
177	molecule{
178	name = "TIP5P";
179
180	atom[0]{
181	type = "O_TIP5P";
182	position( 0.0, 0.0, -0.06556 );
183	}
184	atom[1]{
185	type = "H_TIP5P";
186	position( 0.0, 0.75695, 0.52032 );
187	}
188	atom[2]{
189	type = "H_TIP5P";
190	position( 0.0, -0.75695, 0.52032 );
191	}
192	atom[3]{
193	type = "EP_TIP5P";
194	position( 0.57154, 0.0, -0.46971 );
195	}
196	atom[4]{
197	type = "EP_TIP5P";
198	position( -0.57154, 0.0, -0.46971 );
199	}
200
201	rigidBody[0]{
202
203	members(0, 1, 2, 3, 4);
204	}
205
206
207	cutoffGroup{
208
209	members(0, 1, 2, 3, 4);
210	}
211	}
212
213	molecule{
214	name = "TIP5P-E";
215
216	atom[0]{
217	type = "O_TIP5P-E";
218	position( 0.0, 0.0, -0.06556 );
219	}
220	atom[1]{
221	type = "H_TIP5P";
222	position( 0.0, 0.75695, 0.52032 );
223	}
224	atom[2]{
225	type = "H_TIP5P";
226	position( 0.0, -0.75695, 0.52032 );
227	}
228	atom[3]{
229	type = "EP_TIP5P";
230	position( 0.57154, 0.0, -0.46971 );
231	}
232	atom[4]{
233	type = "EP_TIP5P";
234	position( -0.57154, 0.0, -0.46971 );
235	}
236
237	rigidBody[0]{
238
239	members(0, 1, 2, 3, 4);
240	}
241
242
243	cutoffGroup{
244
245	members(0, 1, 2, 3, 4);
246	}
247	}
248
249	molecule{
250	name = "SPCE";
251
252	atom[0]{
253	type = "O_SPCE";
254	position( 0.0, 0.0, -0.06461 );
255	}
256	atom[1]{
257	type = "H_SPCE";
258	position( 0.0, 0.81649, 0.51275 );
259	}
260	atom[2]{
261	type = "H_SPCE";
262	position( 0.0, -0.81649, 0.51275 );
263	}
264
265	rigidBody[0]{
266
267	members(0, 1, 2);
268	}
269
270
271	cutoffGroup{
272
273	members(0, 1, 2);
274	}
275	}
276
277	molecule{
278	name = "SPC";
279
280	atom[0]{
281	type = "O_SPC";
282	position( 0.0, 0.0, -0.06461 );
283	}
284	atom[1]{
285	type = "H_SPC";
286	position( 0.0, 0.81649, 0.51275 );
287	}
288	atom[2]{
289	type = "H_SPC";
290	position( 0.0, -0.81649, 0.51275 );
291	}
292
293	rigidBody[0]{
294
295	members(0, 1, 2);
296	}
297
298
299	cutoffGroup{
300
301	members(0, 1, 2);
302	}
303	}
304
305	molecule{
306	name = "DPD";
307
308	atom[0]{
309	type = "DPD";
310	position(0.0, 0.0, 0.0);
311	}
312	}
313
314	#endif