water/tap/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 = "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:	2349
Committed:	Thu Oct 6 18:44:32 2005 UTC (18 years, 8 months ago) by chrisfen
File size:	3879 byte(s)
Log Message:	fixing up the samples
#	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 = "SSD_E";
24	nAtoms = 1;
25	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	nAtoms = 1;
35	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	nAtoms = 1;
45	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	nAtoms = 1;
55	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	nAtoms = 3;
65	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	nRigidBodies = 1;
79	rigidBody[0]{
80	nMembers = 3;
81	members(0, 1, 2);
82	}
83
84	nCutoffGroups = 1;
85	cutoffGroup[0]{
86	nMembers = 3;
87	members(0, 1, 2);
88	}
89	}
90
91	molecule{
92	name = "TIP4P";
93	nAtoms = 4;
94	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	nRigidBodies = 1;
111	rigidBody[0]{
112	nMembers = 4;
113	members(0, 1, 2, 3);
114	}
115
116	nCutoffGroups = 1;
117	cutoffGroup[0]{
118	nMembers = 4;
119	members(0, 1, 2, 3);
120	}
121	}
122
123	molecule{
124	name = "TIP4P-Ew";
125	nAtoms = 4;
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	nRigidBodies = 1;
143	rigidBody[0]{
144	nMembers = 4;
145	members(0, 1, 2, 3);
146	}
147
148	nCutoffGroups = 1;
149	cutoffGroup[0]{
150	nMembers = 4;
151	members(0, 1, 2, 3);
152	}
153	}
154
155	molecule{
156	name = "TIP5P";
157	nAtoms = 5;
158	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	nRigidBodies = 1;
179	rigidBody[0]{
180	nMembers = 5;
181	members(0, 1, 2, 3, 4);
182	}
183
184	nCutoffGroups = 1;
185	cutoffGroup[0]{
186	nMembers = 5;
187	members(0, 1, 2, 3, 4);
188	}
189	}
190
191	molecule{
192	name = "SPCE";
193	nAtoms = 3;
194	atom[0]{
195	type = "O_SPCE";
196	position( 0.0, 0.0, -0.06461 );
197	}
198	atom[1]{
199	type = "H_SPCE";
200	position( 0.0, 0.81649, 0.51275 );
201	}
202	atom[2]{
203	type = "H_SPCE";
204	position( 0.0, -0.81649, 0.51275 );
205	}
206	nRigidBodies = 1;
207	rigidBody[0]{
208	nMembers = 3;
209	members(0, 1, 2);
210	}
211
212	nCutoffGroups = 1;
213	cutoffGroup[0]{
214	nMembers = 3;
215	members(0, 1, 2);
216	}
217	}
218
219	molecule{
220	name = "SPC";
221	nAtoms = 3;
222	atom[0]{
223	type = "O_SPC";
224	position( 0.0, 0.0, -0.06461 );
225	}
226	atom[1]{
227	type = "H_SPC";
228	position( 0.0, 0.81649, 0.51275 );
229	}
230	atom[2]{
231	type = "H_SPC";
232	position( 0.0, -0.81649, 0.51275 );
233	}
234	nRigidBodies = 1;
235	rigidBody[0]{
236	nMembers = 3;
237	members(0, 1, 2);
238	}
239
240	nCutoffGroups = 1;
241	cutoffGroup[0]{
242	nMembers = 3;
243	members(0, 1, 2);
244	}
245	}
246
247	molecule{
248	name = "DPD";
249	nAtoms = 1;
250	atom[0]{
251	type = "DPD";
252	position(0.0, 0.0, 0.0);
253	}
254	}
255
256	#endif