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
#	Content
1	#ifndef _WATER_MD_
2	#define _WATER_MD_
3
4	molecule{
5	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	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	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	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	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