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 = "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:	979
Committed:	Thu May 25 21:40:57 2006 UTC (18 years, 11 months ago) by chrisfen
Original Path:	*trunk/samples/thermoIntegration/liquid/water.md*
File size:	3885 byte(s)
Log Message:	Added TIP5P-E and fixed a bug for Thermodynamic integration (you can now have a lambda of 0)
#	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			name = "TIP3P";
64	tim	790
65	chrisfen	437	atom[0]{
66			type = "O_TIP3P";
67			position( 0.0, 0.0, -0.06556 );
68			}
69			atom[1]{
70			type = "H_TIP3P";
71			position( 0.0, 0.75695, 0.52032 );
72			}
73			atom[2]{
74			type = "H_TIP3P";
75			position( 0.0, -0.75695, 0.52032 );
76			}
77
78	tim	790
79	chrisfen	437	rigidBody[0]{
80	tim	790
81	chrisfen	437	members(0, 1, 2);
82			}
83
84	tim	790
85			cutoffGroup{
86
87	chrisfen	437	members(0, 1, 2);
88			}
89			}
90
91			molecule{
92			name = "TIP4P";
93	tim	790
94	chrisfen	437	atom[0]{
95			type = "O_TIP4P";
96			position( 0.0, 0.0, -0.06556 );
97			}
98			atom[1]{
99			type = "H_TIP4P";
100			position( 0.0, 0.75695, 0.52032 );
101			}
102			atom[2]{
103			type = "H_TIP4P";
104			position( 0.0, -0.75695, 0.52032 );
105			}
106			atom[3]{
107			type = "EP_TIP4P";
108			position( 0.0, 0.0, 0.08444 );
109			}
110	tim	790
111	chrisfen	437	rigidBody[0]{
112	tim	790
113	chrisfen	437	members(0, 1, 2, 3);
114			}
115
116	tim	790
117			cutoffGroup{
118
119	chrisfen	437	members(0, 1, 2, 3);
120			}
121			}
122
123			molecule{
124	chrisfen	979	name = "TIP4P-Ew";
125
126			atom[0]{
127			type = "O_TIP4P-Ew";
128			position( 0.0, 0.0, -0.06556 );
129			}
130			atom[1]{
131			type = "H_TIP4P-Ew";
132			position( 0.0, 0.75695, 0.52032 );
133			}
134			atom[2]{
135			type = "H_TIP4P-Ew";
136			position( 0.0, -0.75695, 0.52032 );
137			}
138			atom[3]{
139			type = "EP_TIP4P-Ew";
140			position( 0.0, 0.0, 0.05944 );
141			}
142
143			rigidBody[0]{
144
145			members(0, 1, 2, 3);
146			}
147
148
149			cutoffGroup{
150
151			members(0, 1, 2, 3);
152			}
153			}
154
155			molecule{
156	chrisfen	437	name = "TIP5P";
157	tim	790
158	chrisfen	437	atom[0]{
159			type = "O_TIP5P";
160			position( 0.0, 0.0, -0.06556 );
161			}
162			atom[1]{
163			type = "H_TIP5P";
164			position( 0.0, 0.75695, 0.52032 );
165			}
166			atom[2]{
167			type = "H_TIP5P";
168			position( 0.0, -0.75695, 0.52032 );
169			}
170			atom[3]{
171			type = "EP_TIP5P";
172			position( 0.57154, 0.0, -0.46971 );
173			}
174			atom[4]{
175			type = "EP_TIP5P";
176			position( -0.57154, 0.0, -0.46971 );
177			}
178	tim	790
179	chrisfen	437	rigidBody[0]{
180	tim	790
181	chrisfen	437	members(0, 1, 2, 3, 4);
182			}
183
184	tim	790
185			cutoffGroup{
186
187	chrisfen	437	members(0, 1, 2, 3, 4);
188			}
189			}
190
191			molecule{
192	chrisfen	979	name = "TIP5P-E";
193
194			atom[0]{
195			type = "O_TIP5P-E";
196			position( 0.0, 0.0, -0.06556 );
197			}
198			atom[1]{
199			type = "H_TIP5P";
200			position( 0.0, 0.75695, 0.52032 );
201			}
202			atom[2]{
203			type = "H_TIP5P";
204			position( 0.0, -0.75695, 0.52032 );
205			}
206			atom[3]{
207			type = "EP_TIP5P";
208			position( 0.57154, 0.0, -0.46971 );
209			}
210			atom[4]{
211			type = "EP_TIP5P";
212			position( -0.57154, 0.0, -0.46971 );
213			}
214
215			rigidBody[0]{
216
217			members(0, 1, 2, 3, 4);
218			}
219
220
221			cutoffGroup{
222
223			members(0, 1, 2, 3, 4);
224			}
225			}
226
227			molecule{
228	chrisfen	437	name = "SPCE";
229	tim	790
230	chrisfen	437	atom[0]{
231			type = "O_SPCE";
232			position( 0.0, 0.0, -0.06461 );
233			}
234			atom[1]{
235			type = "H_SPCE";
236			position( 0.0, 0.81649, 0.51275 );
237			}
238			atom[2]{
239			type = "H_SPCE";
240			position( 0.0, -0.81649, 0.51275 );
241			}
242	tim	790
243	chrisfen	437	rigidBody[0]{
244	tim	790
245	chrisfen	437	members(0, 1, 2);
246			}
247
248	tim	790
249			cutoffGroup{
250
251	chrisfen	437	members(0, 1, 2);
252			}
253			}
254
255			molecule{
256			name = "SPC";
257	tim	790
258	chrisfen	437	atom[0]{
259			type = "O_SPC";
260			position( 0.0, 0.0, -0.06461 );
261			}
262			atom[1]{
263			type = "H_SPC";
264			position( 0.0, 0.81649, 0.51275 );
265			}
266			atom[2]{
267			type = "H_SPC";
268			position( 0.0, -0.81649, 0.51275 );
269			}
270	tim	790
271	chrisfen	437	rigidBody[0]{
272	tim	790
273	chrisfen	437	members(0, 1, 2);
274			}
275
276	tim	790
277			cutoffGroup{
278
279	chrisfen	437	members(0, 1, 2);
280			}
281			}
282
283			molecule{
284			name = "DPD";
285	tim	790
286	chrisfen	437	atom[0]{
287			type = "DPD";
288			position(0.0, 0.0, 0.0);
289			}
290			}
291
292			#endif