thermoIntegration/liquid/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:	1009
Committed:	Wed Jul 19 12:46:20 2006 UTC (18 years, 9 months ago) by chrisfen
File size:	4164 byte(s)
Log Message:	Added tred to sample water.md files
#	User	Rev	Content
1	chrisfen	437	#ifndef _WATER_MD_
2			#define _WATER_MD_
3
4			molecule{
5	chrisfen	979	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	chrisfen	437	name = "SSD_E";
24	tim	790
25	chrisfen	437	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	chrisfen	437	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	chrisfen	437	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	chrisfen	437	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	chrisfen	1009	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	chrisfen	437	name = "TIP3P";
86	tim	790
87	chrisfen	437	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	tim	790
101	chrisfen	437	rigidBody[0]{
102	tim	790
103	chrisfen	437	members(0, 1, 2);
104			}
105
106	tim	790
107			cutoffGroup{
108
109	chrisfen	437	members(0, 1, 2);
110			}
111			}
112
113			molecule{
114			name = "TIP4P";
115	tim	790
116	chrisfen	437	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	tim	790
133	chrisfen	437	rigidBody[0]{
134	tim	790
135	chrisfen	437	members(0, 1, 2, 3);
136			}
137
138	tim	790
139			cutoffGroup{
140
141	chrisfen	437	members(0, 1, 2, 3);
142			}
143			}
144
145			molecule{
146	chrisfen	979	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	chrisfen	437	name = "TIP5P";
179	tim	790
180	chrisfen	437	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	tim	790
201	chrisfen	437	rigidBody[0]{
202	tim	790
203	chrisfen	437	members(0, 1, 2, 3, 4);
204			}
205
206	tim	790
207			cutoffGroup{
208
209	chrisfen	437	members(0, 1, 2, 3, 4);
210			}
211			}
212
213			molecule{
214	chrisfen	979	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	chrisfen	437	name = "SPCE";
251	tim	790
252	chrisfen	437	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	tim	790
265	chrisfen	437	rigidBody[0]{
266	tim	790
267	chrisfen	437	members(0, 1, 2);
268			}
269
270	tim	790
271			cutoffGroup{
272
273	chrisfen	437	members(0, 1, 2);
274			}
275			}
276
277			molecule{
278			name = "SPC";
279	tim	790
280	chrisfen	437	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	tim	790
293	chrisfen	437	rigidBody[0]{
294	tim	790
295	chrisfen	437	members(0, 1, 2);
296			}
297
298	tim	790
299			cutoffGroup{
300
301	chrisfen	437	members(0, 1, 2);
302			}
303			}
304
305			molecule{
306			name = "DPD";
307	tim	790
308	chrisfen	437	atom[0]{
309			type = "DPD";
310			position(0.0, 0.0, 0.0);
311			}
312			}
313
314			#endif