water/ssdrf/water.md

#ifndef _WATER_MD_
#define _WATER_MD_

molecule{
  name = "Cl-";
  nAtoms = 1;
  atom[0]{
    type = "Cl-";
    position(0.0, 0.0, 0.0);
  }
}

molecule{
  name = "Na+";
  nAtoms = 1;
  atom[0]{
    type = "Na+";
    position(0.0, 0.0, 0.0);
  }
}

molecule{
  name = "PAIR";
  nAtoms = 3;
  atom[0]{
    type = "Pchg+";
    position(0.0, 1, 1.0);
  }
  atom[1]{
    type = "Pchg+";
    position(0.0, -1, 1.0);
  }
  atom[2]{
    type = "Pchg-";
    position(0.0, 0.0, -1.0);
  }

  nRigidBodies = 1;
  rigidBody[0]{ 
    nMembers = 3;
    members(0, 1, 2);
  }

  nCutoffGroups = 1;
  cutoffGroup[0]{
    nMembers = 3;
    members(0, 1, 2);
  }
}

molecule{
  name = "PDIP";
  nAtoms = 1;
  atom[0]{
    type = "PDIP";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
}

molecule{
  name = "SSD_E";
  nAtoms = 1;
  atom[0]{
    type = "SSD_E";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
}

molecule{
  name = "SSD_RF";
  nAtoms = 1;
  atom[0]{
    type = "SSD_RF";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
}

molecule{
  name = "SSD";
  nAtoms = 1;
  atom[0]{
    type = "SSD";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
}

molecule{
  name = "SSD1";
  nAtoms = 1;
  atom[0]{
    type = "SSD1";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
}

molecule{
  name = "TIP3P";
  nAtoms = 3;
  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 );
  }

  nRigidBodies = 1;
  rigidBody[0]{ 
    nMembers = 3;
    members(0, 1, 2);
  }

  nCutoffGroups = 1;
  cutoffGroup[0]{
    nMembers = 3;
    members(0, 1, 2);
  }
}

molecule{
  name = "TIP4P";
  nAtoms = 4;
  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 );
  }
  nRigidBodies = 1;
  rigidBody[0]{
    nMembers = 4;
    members(0, 1, 2, 3);
  }

  nCutoffGroups = 1;
  cutoffGroup[0]{
    nMembers = 4;
    members(0, 1, 2, 3);
  }
}

molecule{
  name = "TIP4P-Ew";
  nAtoms = 4;
  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 );
  }
  nRigidBodies = 1;
  rigidBody[0]{
    nMembers = 4;
    members(0, 1, 2, 3);
  }

  nCutoffGroups = 1;
  cutoffGroup[0]{
    nMembers = 4;
    members(0, 1, 2, 3);
  }
}

molecule{
  name = "TIP5P";
  nAtoms = 5;
  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 );
  }
  nRigidBodies = 1;
  rigidBody[0]{
    nMembers = 5;
    members(0, 1, 2, 3, 4);
  }

  nCutoffGroups = 1;
  cutoffGroup[0]{
    nMembers = 5;
    members(0, 1, 2, 3, 4);
  }
}

molecule{
  name = "SPCE";
  nAtoms = 3;
  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 );
  }
  nRigidBodies = 1;
  rigidBody[0]{
    nMembers = 3;
    members(0, 1, 2);
  }

  nCutoffGroups = 1;
  cutoffGroup[0]{
    nMembers = 3;
    members(0, 1, 2);
  }
}

molecule{
  name = "SPC";
  nAtoms = 3;
  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 );
  }
  nRigidBodies = 1;
  rigidBody[0]{
    nMembers = 3;
    members(0, 1, 2);
  }

  nCutoffGroups = 1;
  cutoffGroup[0]{
    nMembers = 3;
    members(0, 1, 2);
  }
}

molecule{
  name = "DPD";
  nAtoms = 1;
  atom[0]{
    type = "DPD";
    position(0.0, 0.0, 0.0);
  }
}

#endif
Revision:	2397
Committed:	Wed Oct 26 23:30:52 2005 UTC (18 years, 8 months ago) by chrisfen
File size:	4422 byte(s)
Log Message:	added a test molecule
#	User	Rev	Content
1	chrisfen	2059	#ifndef _WATER_MD_
2			#define _WATER_MD_
3
4			molecule{
5	chrisfen	2349	name = "Cl-";
6			nAtoms = 1;
7			atom[0]{
8			type = "Cl-";
9			position(0.0, 0.0, 0.0);
10			}
11			}
12
13			molecule{
14			name = "Na+";
15			nAtoms = 1;
16			atom[0]{
17			type = "Na+";
18			position(0.0, 0.0, 0.0);
19			}
20			}
21
22			molecule{
23	chrisfen	2397	name = "PAIR";
24			nAtoms = 3;
25			atom[0]{
26			type = "Pchg+";
27			position(0.0, 1, 1.0);
28			}
29			atom[1]{
30			type = "Pchg+";
31			position(0.0, -1, 1.0);
32			}
33			atom[2]{
34			type = "Pchg-";
35			position(0.0, 0.0, -1.0);
36			}
37
38			nRigidBodies = 1;
39			rigidBody[0]{
40			nMembers = 3;
41			members(0, 1, 2);
42			}
43
44			nCutoffGroups = 1;
45			cutoffGroup[0]{
46			nMembers = 3;
47			members(0, 1, 2);
48			}
49			}
50
51			molecule{
52			name = "PDIP";
53			nAtoms = 1;
54			atom[0]{
55			type = "PDIP";
56			position( 0.0, 0.0, 0.0 );
57			orientation( 0.0, 0.0, 0.0 );
58			}
59			}
60
61			molecule{
62	chrisfen	2059	name = "SSD_E";
63			nAtoms = 1;
64			atom[0]{
65			type = "SSD_E";
66			position( 0.0, 0.0, 0.0 );
67			orientation( 0.0, 0.0, 0.0 );
68			}
69			}
70
71			molecule{
72			name = "SSD_RF";
73			nAtoms = 1;
74			atom[0]{
75			type = "SSD_RF";
76			position( 0.0, 0.0, 0.0 );
77			orientation( 0.0, 0.0, 0.0 );
78			}
79			}
80
81			molecule{
82			name = "SSD";
83			nAtoms = 1;
84			atom[0]{
85			type = "SSD";
86			position( 0.0, 0.0, 0.0 );
87			orientation( 0.0, 0.0, 0.0 );
88			}
89			}
90
91			molecule{
92			name = "SSD1";
93			nAtoms = 1;
94			atom[0]{
95			type = "SSD1";
96			position( 0.0, 0.0, 0.0 );
97			orientation( 0.0, 0.0, 0.0 );
98			}
99			}
100
101			molecule{
102			name = "TIP3P";
103			nAtoms = 3;
104			atom[0]{
105			type = "O_TIP3P";
106			position( 0.0, 0.0, -0.06556 );
107			}
108			atom[1]{
109			type = "H_TIP3P";
110			position( 0.0, 0.75695, 0.52032 );
111			}
112			atom[2]{
113			type = "H_TIP3P";
114			position( 0.0, -0.75695, 0.52032 );
115			}
116
117			nRigidBodies = 1;
118			rigidBody[0]{
119			nMembers = 3;
120			members(0, 1, 2);
121			}
122
123			nCutoffGroups = 1;
124			cutoffGroup[0]{
125			nMembers = 3;
126			members(0, 1, 2);
127			}
128			}
129
130			molecule{
131			name = "TIP4P";
132			nAtoms = 4;
133			atom[0]{
134			type = "O_TIP4P";
135			position( 0.0, 0.0, -0.06556 );
136			}
137			atom[1]{
138			type = "H_TIP4P";
139			position( 0.0, 0.75695, 0.52032 );
140			}
141			atom[2]{
142			type = "H_TIP4P";
143			position( 0.0, -0.75695, 0.52032 );
144			}
145			atom[3]{
146			type = "EP_TIP4P";
147			position( 0.0, 0.0, 0.08444 );
148			}
149			nRigidBodies = 1;
150			rigidBody[0]{
151			nMembers = 4;
152			members(0, 1, 2, 3);
153			}
154
155			nCutoffGroups = 1;
156			cutoffGroup[0]{
157			nMembers = 4;
158			members(0, 1, 2, 3);
159			}
160			}
161
162			molecule{
163	chrisfen	2216	name = "TIP4P-Ew";
164			nAtoms = 4;
165			atom[0]{
166			type = "O_TIP4P-Ew";
167			position( 0.0, 0.0, -0.06556 );
168			}
169			atom[1]{
170			type = "H_TIP4P-Ew";
171			position( 0.0, 0.75695, 0.52032 );
172			}
173			atom[2]{
174			type = "H_TIP4P-Ew";
175			position( 0.0, -0.75695, 0.52032 );
176			}
177			atom[3]{
178			type = "EP_TIP4P-Ew";
179			position( 0.0, 0.0, 0.05944 );
180			}
181			nRigidBodies = 1;
182			rigidBody[0]{
183			nMembers = 4;
184			members(0, 1, 2, 3);
185			}
186
187			nCutoffGroups = 1;
188			cutoffGroup[0]{
189			nMembers = 4;
190			members(0, 1, 2, 3);
191			}
192			}
193
194			molecule{
195	chrisfen	2059	name = "TIP5P";
196			nAtoms = 5;
197			atom[0]{
198			type = "O_TIP5P";
199			position( 0.0, 0.0, -0.06556 );
200			}
201			atom[1]{
202			type = "H_TIP5P";
203			position( 0.0, 0.75695, 0.52032 );
204			}
205			atom[2]{
206			type = "H_TIP5P";
207			position( 0.0, -0.75695, 0.52032 );
208			}
209			atom[3]{
210			type = "EP_TIP5P";
211			position( 0.57154, 0.0, -0.46971 );
212			}
213			atom[4]{
214			type = "EP_TIP5P";
215			position( -0.57154, 0.0, -0.46971 );
216			}
217			nRigidBodies = 1;
218			rigidBody[0]{
219			nMembers = 5;
220			members(0, 1, 2, 3, 4);
221			}
222
223			nCutoffGroups = 1;
224			cutoffGroup[0]{
225			nMembers = 5;
226			members(0, 1, 2, 3, 4);
227			}
228			}
229
230			molecule{
231			name = "SPCE";
232			nAtoms = 3;
233			atom[0]{
234			type = "O_SPCE";
235			position( 0.0, 0.0, -0.06461 );
236			}
237			atom[1]{
238			type = "H_SPCE";
239			position( 0.0, 0.81649, 0.51275 );
240			}
241			atom[2]{
242			type = "H_SPCE";
243			position( 0.0, -0.81649, 0.51275 );
244			}
245			nRigidBodies = 1;
246			rigidBody[0]{
247			nMembers = 3;
248			members(0, 1, 2);
249			}
250
251			nCutoffGroups = 1;
252			cutoffGroup[0]{
253			nMembers = 3;
254			members(0, 1, 2);
255			}
256			}
257
258			molecule{
259			name = "SPC";
260			nAtoms = 3;
261			atom[0]{
262			type = "O_SPC";
263			position( 0.0, 0.0, -0.06461 );
264			}
265			atom[1]{
266			type = "H_SPC";
267			position( 0.0, 0.81649, 0.51275 );
268			}
269			atom[2]{
270			type = "H_SPC";
271			position( 0.0, -0.81649, 0.51275 );
272			}
273			nRigidBodies = 1;
274			rigidBody[0]{
275			nMembers = 3;
276			members(0, 1, 2);
277			}
278
279			nCutoffGroups = 1;
280			cutoffGroup[0]{
281			nMembers = 3;
282			members(0, 1, 2);
283			}
284			}
285
286			molecule{
287			name = "DPD";
288			nAtoms = 1;
289			atom[0]{
290			type = "DPD";
291			position(0.0, 0.0, 0.0);
292			}
293			}
294
295			#endif