water/ssde/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_Q";
  
  atom[0]{
    type = "SSD_Q";
    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:	1820
Committed:	Tue Dec 18 16:23:13 2012 UTC (12 years, 7 months ago) by gezelter
File size:	3882 byte(s)
Log Message:	New electrostatic bug fixes.
#	User	Rev	Content
1	gezelter	2	#ifndef _WATER_MD_
2			#define _WATER_MD_
3
4			molecule{
5	chrisfen	650	name = "Cl-";
6	tim	790
7	chrisfen	650	atom[0]{
8			type = "Cl-";
9			position(0.0, 0.0, 0.0);
10			}
11			}
12
13			molecule{
14			name = "Na+";
15	tim	790
16	chrisfen	650	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	gezelter	1820	molecule{
32			name = "SSD_Q";
33
34			atom[0]{
35			type = "SSD_Q";
36			position( 0.0, 0.0, 0.0 );
37			orientation( 0.0, 0.0, 0.0 );
38			}
39			}
40	gezelter	2
41			molecule{
42			name = "SSD_RF";
43	tim	790
44	gezelter	2	atom[0]{
45			type = "SSD_RF";
46			position( 0.0, 0.0, 0.0 );
47			orientation( 0.0, 0.0, 0.0 );
48			}
49			}
50
51			molecule{
52			name = "SSD";
53	tim	790
54	gezelter	2	atom[0]{
55			type = "SSD";
56			position( 0.0, 0.0, 0.0 );
57			orientation( 0.0, 0.0, 0.0 );
58			}
59			}
60
61			molecule{
62			name = "SSD1";
63	tim	790
64	gezelter	2	atom[0]{
65			type = "SSD1";
66			position( 0.0, 0.0, 0.0 );
67			orientation( 0.0, 0.0, 0.0 );
68			}
69			}
70
71			molecule{
72	chrisfen	1009	name = "TRED";
73
74			atom[0]{
75			type = "TRED";
76			position( 0.0, 0.0, 0.0 );
77			orientation( 0.0, 0.0, 0.0 );
78			}
79			atom[1]{
80			type = "EP_TRED";
81			position( 0.0, 0.0, 0.5 );
82			}
83
84			rigidBody[0]{
85			members(0, 1);
86			}
87			}
88
89			molecule{
90	gezelter	2	name = "TIP3P";
91	tim	790
92	gezelter	2	atom[0]{
93			type = "O_TIP3P";
94			position( 0.0, 0.0, -0.06556 );
95			}
96			atom[1]{
97			type = "H_TIP3P";
98			position( 0.0, 0.75695, 0.52032 );
99			}
100			atom[2]{
101			type = "H_TIP3P";
102			position( 0.0, -0.75695, 0.52032 );
103			}
104	tim	790
105	gezelter	1393	rigidBody[0]{
106	gezelter	2	members(0, 1, 2);
107	gezelter	1393	}
108	gezelter	2	}
109
110			molecule{
111			name = "TIP4P";
112	tim	790
113	gezelter	2	atom[0]{
114			type = "O_TIP4P";
115			position( 0.0, 0.0, -0.06556 );
116			}
117			atom[1]{
118			type = "H_TIP4P";
119			position( 0.0, 0.75695, 0.52032 );
120			}
121			atom[2]{
122			type = "H_TIP4P";
123			position( 0.0, -0.75695, 0.52032 );
124			}
125			atom[3]{
126			type = "EP_TIP4P";
127			position( 0.0, 0.0, 0.08444 );
128			}
129	tim	790
130	gezelter	1393	rigidBody[0]{
131	gezelter	2	members(0, 1, 2, 3);
132	gezelter	1393	}
133	gezelter	2	}
134
135			molecule{
136	chrisfen	519	name = "TIP4P-Ew";
137	tim	790
138	chrisfen	519	atom[0]{
139			type = "O_TIP4P-Ew";
140			position( 0.0, 0.0, -0.06556 );
141			}
142			atom[1]{
143			type = "H_TIP4P-Ew";
144			position( 0.0, 0.75695, 0.52032 );
145			}
146			atom[2]{
147			type = "H_TIP4P-Ew";
148			position( 0.0, -0.75695, 0.52032 );
149			}
150			atom[3]{
151			type = "EP_TIP4P-Ew";
152			position( 0.0, 0.0, 0.05944 );
153			}
154	tim	790
155	gezelter	1393	rigidBody[0]{
156	chrisfen	519	members(0, 1, 2, 3);
157			}
158			}
159
160			molecule{
161	gezelter	2	name = "TIP5P";
162	tim	790
163	gezelter	2	atom[0]{
164			type = "O_TIP5P";
165			position( 0.0, 0.0, -0.06556 );
166			}
167			atom[1]{
168			type = "H_TIP5P";
169			position( 0.0, 0.75695, 0.52032 );
170			}
171			atom[2]{
172			type = "H_TIP5P";
173			position( 0.0, -0.75695, 0.52032 );
174			}
175			atom[3]{
176			type = "EP_TIP5P";
177			position( 0.57154, 0.0, -0.46971 );
178			}
179			atom[4]{
180			type = "EP_TIP5P";
181			position( -0.57154, 0.0, -0.46971 );
182			}
183	tim	790
184	gezelter	2	rigidBody[0]{
185			members(0, 1, 2, 3, 4);
186			}
187			}
188
189			molecule{
190	chrisfen	979	name = "TIP5P-E";
191
192			atom[0]{
193			type = "O_TIP5P-E";
194			position( 0.0, 0.0, -0.06556 );
195			}
196			atom[1]{
197			type = "H_TIP5P";
198			position( 0.0, 0.75695, 0.52032 );
199			}
200			atom[2]{
201			type = "H_TIP5P";
202			position( 0.0, -0.75695, 0.52032 );
203			}
204			atom[3]{
205			type = "EP_TIP5P";
206			position( 0.57154, 0.0, -0.46971 );
207			}
208			atom[4]{
209			type = "EP_TIP5P";
210			position( -0.57154, 0.0, -0.46971 );
211			}
212
213	gezelter	1393	rigidBody[0]{
214	chrisfen	979	members(0, 1, 2, 3, 4);
215			}
216			}
217
218			molecule{
219	gezelter	2	name = "SPCE";
220	tim	790
221	gezelter	2	atom[0]{
222			type = "O_SPCE";
223			position( 0.0, 0.0, -0.06461 );
224			}
225			atom[1]{
226			type = "H_SPCE";
227			position( 0.0, 0.81649, 0.51275 );
228			}
229			atom[2]{
230			type = "H_SPCE";
231			position( 0.0, -0.81649, 0.51275 );
232			}
233	tim	790
234	gezelter	1393	rigidBody[0]{
235	gezelter	2	members(0, 1, 2);
236			}
237			}
238
239			molecule{
240			name = "SPC";
241	tim	790
242	gezelter	2	atom[0]{
243			type = "O_SPC";
244			position( 0.0, 0.0, -0.06461 );
245			}
246			atom[1]{
247			type = "H_SPC";
248			position( 0.0, 0.81649, 0.51275 );
249			}
250			atom[2]{
251			type = "H_SPC";
252			position( 0.0, -0.81649, 0.51275 );
253			}
254	tim	790
255	gezelter	1393	rigidBody[0]{
256	gezelter	2	members(0, 1, 2);
257			}
258			}
259
260			molecule{
261			name = "DPD";
262	tim	790
263	gezelter	2	atom[0]{
264			type = "DPD";
265			position(0.0, 0.0, 0.0);
266			}
267			}
268
269			#endif