water/ssdq/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 = "SSDQ";
  
  atom[0]{
    type = "SSDQ";
    position( 0.0, 0.0, 0.0 );
    orientation( 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:	1958
Committed:	Mon Dec 16 21:18:43 2013 UTC (11 years, 8 months ago) by gezelter
File size:	3881 byte(s)
Log Message:	Adding SSDQ model to test the electrostatics code
#	User	Rev	Content
1	gezelter	1958	#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 = "SSDQ";
24
25			atom[0]{
26			type = "SSDQ";
27			position( 0.0, 0.0, 0.0 );
28			orientation( 0.0, 0.0, 0.0 );
29			}
30			}
31
32			molecule{
33			name = "SSD_E";
34
35			atom[0]{
36			type = "SSD_E";
37			position( 0.0, 0.0, 0.0 );
38			orientation( 0.0, 0.0, 0.0 );
39			}
40			}
41
42			molecule{
43			name = "SSD_RF";
44
45			atom[0]{
46			type = "SSD_RF";
47			position( 0.0, 0.0, 0.0 );
48			orientation( 0.0, 0.0, 0.0 );
49			}
50			}
51
52			molecule{
53			name = "SSD";
54
55			atom[0]{
56			type = "SSD";
57			position( 0.0, 0.0, 0.0 );
58			orientation( 0.0, 0.0, 0.0 );
59			}
60			}
61
62			molecule{
63			name = "SSD1";
64
65			atom[0]{
66			type = "SSD1";
67			position( 0.0, 0.0, 0.0 );
68			orientation( 0.0, 0.0, 0.0 );
69			}
70			}
71
72			molecule{
73			name = "TRED";
74
75			atom[0]{
76			type = "TRED";
77			position( 0.0, 0.0, 0.0 );
78			orientation( 0.0, 0.0, 0.0 );
79			}
80			atom[1]{
81			type = "EP_TRED";
82			position( 0.0, 0.0, 0.5 );
83			}
84
85			rigidBody[0]{
86			members(0, 1);
87			}
88			}
89
90			molecule{
91			name = "TIP3P";
92
93			atom[0]{
94			type = "O_TIP3P";
95			position( 0.0, 0.0, -0.06556 );
96			}
97			atom[1]{
98			type = "H_TIP3P";
99			position( 0.0, 0.75695, 0.52032 );
100			}
101			atom[2]{
102			type = "H_TIP3P";
103			position( 0.0, -0.75695, 0.52032 );
104			}
105
106			rigidBody[0]{
107			members(0, 1, 2);
108			}
109			}
110
111			molecule{
112			name = "TIP4P";
113
114			atom[0]{
115			type = "O_TIP4P";
116			position( 0.0, 0.0, -0.06556 );
117			}
118			atom[1]{
119			type = "H_TIP4P";
120			position( 0.0, 0.75695, 0.52032 );
121			}
122			atom[2]{
123			type = "H_TIP4P";
124			position( 0.0, -0.75695, 0.52032 );
125			}
126			atom[3]{
127			type = "EP_TIP4P";
128			position( 0.0, 0.0, 0.08444 );
129			}
130
131			rigidBody[0]{
132			members(0, 1, 2, 3);
133			}
134			}
135
136			molecule{
137			name = "TIP4P-Ew";
138
139			atom[0]{
140			type = "O_TIP4P-Ew";
141			position( 0.0, 0.0, -0.06556 );
142			}
143			atom[1]{
144			type = "H_TIP4P-Ew";
145			position( 0.0, 0.75695, 0.52032 );
146			}
147			atom[2]{
148			type = "H_TIP4P-Ew";
149			position( 0.0, -0.75695, 0.52032 );
150			}
151			atom[3]{
152			type = "EP_TIP4P-Ew";
153			position( 0.0, 0.0, 0.05944 );
154			}
155
156			rigidBody[0]{
157			members(0, 1, 2, 3);
158			}
159			}
160
161			molecule{
162			name = "TIP5P";
163
164			atom[0]{
165			type = "O_TIP5P";
166			position( 0.0, 0.0, -0.06556 );
167			}
168			atom[1]{
169			type = "H_TIP5P";
170			position( 0.0, 0.75695, 0.52032 );
171			}
172			atom[2]{
173			type = "H_TIP5P";
174			position( 0.0, -0.75695, 0.52032 );
175			}
176			atom[3]{
177			type = "EP_TIP5P";
178			position( 0.57154, 0.0, -0.46971 );
179			}
180			atom[4]{
181			type = "EP_TIP5P";
182			position( -0.57154, 0.0, -0.46971 );
183			}
184
185			rigidBody[0]{
186			members(0, 1, 2, 3, 4);
187			}
188			}
189
190			molecule{
191			name = "TIP5P-E";
192
193			atom[0]{
194			type = "O_TIP5P-E";
195			position( 0.0, 0.0, -0.06556 );
196			}
197			atom[1]{
198			type = "H_TIP5P";
199			position( 0.0, 0.75695, 0.52032 );
200			}
201			atom[2]{
202			type = "H_TIP5P";
203			position( 0.0, -0.75695, 0.52032 );
204			}
205			atom[3]{
206			type = "EP_TIP5P";
207			position( 0.57154, 0.0, -0.46971 );
208			}
209			atom[4]{
210			type = "EP_TIP5P";
211			position( -0.57154, 0.0, -0.46971 );
212			}
213
214			rigidBody[0]{
215			members(0, 1, 2, 3, 4);
216			}
217			}
218
219			molecule{
220			name = "SPCE";
221
222			atom[0]{
223			type = "O_SPCE";
224			position( 0.0, 0.0, -0.06461 );
225			}
226			atom[1]{
227			type = "H_SPCE";
228			position( 0.0, 0.81649, 0.51275 );
229			}
230			atom[2]{
231			type = "H_SPCE";
232			position( 0.0, -0.81649, 0.51275 );
233			}
234
235			rigidBody[0]{
236			members(0, 1, 2);
237			}
238			}
239
240			molecule{
241			name = "SPC";
242
243			atom[0]{
244			type = "O_SPC";
245			position( 0.0, 0.0, -0.06461 );
246			}
247			atom[1]{
248			type = "H_SPC";
249			position( 0.0, 0.81649, 0.51275 );
250			}
251			atom[2]{
252			type = "H_SPC";
253			position( 0.0, -0.81649, 0.51275 );
254			}
255
256			rigidBody[0]{
257			members(0, 1, 2);
258			}
259			}
260
261			molecule{
262			name = "DPD";
263
264			atom[0]{
265			type = "DPD";
266			position(0.0, 0.0, 0.0);
267			}
268			}
269
270			#endif