water/ssde/water.md

#ifndef _WATER_MD_
#define _WATER_MD_

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 = "SHED";
  nAtoms = 1;
  atom[0]{
    type = "SHED";
    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:	2220
Committed:	Thu May 5 14:47:35 2005 UTC (19 years, 2 months ago) by chrisfen
File size:	3812 byte(s)
Log Message:	OOPSE setup for TAP water. It's not parametrized, but OOPSE will now let me run it...
#	Content
1	#ifndef _WATER_MD_
2	#define _WATER_MD_
3
4	molecule{
5	name = "SSD_E";
6	nAtoms = 1;
7	atom[0]{
8	type = "SSD_E";
9	position( 0.0, 0.0, 0.0 );
10	orientation( 0.0, 0.0, 0.0 );
11	}
12	}
13
14	molecule{
15	name = "SSD_RF";
16	nAtoms = 1;
17	atom[0]{
18	type = "SSD_RF";
19	position( 0.0, 0.0, 0.0 );
20	orientation( 0.0, 0.0, 0.0 );
21	}
22	}
23
24	molecule{
25	name = "SSD";
26	nAtoms = 1;
27	atom[0]{
28	type = "SSD";
29	position( 0.0, 0.0, 0.0 );
30	orientation( 0.0, 0.0, 0.0 );
31	}
32	}
33
34	molecule{
35	name = "SSD1";
36	nAtoms = 1;
37	atom[0]{
38	type = "SSD1";
39	position( 0.0, 0.0, 0.0 );
40	orientation( 0.0, 0.0, 0.0 );
41	}
42	}
43
44	molecule{
45	name = "SHED";
46	nAtoms = 1;
47	atom[0]{
48	type = "SHED";
49	position( 0.0, 0.0, 0.0 );
50	orientation( 0.0, 0.0, 0.0 );
51	}
52	}
53
54	molecule{
55	name = "TIP3P";
56	nAtoms = 3;
57	atom[0]{
58	type = "O_TIP3P";
59	position( 0.0, 0.0, -0.06556 );
60	}
61	atom[1]{
62	type = "H_TIP3P";
63	position( 0.0, 0.75695, 0.52032 );
64	}
65	atom[2]{
66	type = "H_TIP3P";
67	position( 0.0, -0.75695, 0.52032 );
68	}
69
70	nRigidBodies = 1;
71	rigidBody[0]{
72	nMembers = 3;
73	members(0, 1, 2);
74	}
75
76	nCutoffGroups = 1;
77	cutoffGroup[0]{
78	nMembers = 3;
79	members(0, 1, 2);
80	}
81	}
82
83	molecule{
84	name = "TIP4P";
85	nAtoms = 4;
86	atom[0]{
87	type = "O_TIP4P";
88	position( 0.0, 0.0, -0.06556 );
89	}
90	atom[1]{
91	type = "H_TIP4P";
92	position( 0.0, 0.75695, 0.52032 );
93	}
94	atom[2]{
95	type = "H_TIP4P";
96	position( 0.0, -0.75695, 0.52032 );
97	}
98	atom[3]{
99	type = "EP_TIP4P";
100	position( 0.0, 0.0, 0.08444 );
101	}
102	nRigidBodies = 1;
103	rigidBody[0]{
104	nMembers = 4;
105	members(0, 1, 2, 3);
106	}
107
108	nCutoffGroups = 1;
109	cutoffGroup[0]{
110	nMembers = 4;
111	members(0, 1, 2, 3);
112	}
113	}
114
115	molecule{
116	name = "TIP4P-Ew";
117	nAtoms = 4;
118	atom[0]{
119	type = "O_TIP4P-Ew";
120	position( 0.0, 0.0, -0.06556 );
121	}
122	atom[1]{
123	type = "H_TIP4P-Ew";
124	position( 0.0, 0.75695, 0.52032 );
125	}
126	atom[2]{
127	type = "H_TIP4P-Ew";
128	position( 0.0, -0.75695, 0.52032 );
129	}
130	atom[3]{
131	type = "EP_TIP4P-Ew";
132	position( 0.0, 0.0, 0.05944 );
133	}
134	nRigidBodies = 1;
135	rigidBody[0]{
136	nMembers = 4;
137	members(0, 1, 2, 3);
138	}
139
140	nCutoffGroups = 1;
141	cutoffGroup[0]{
142	nMembers = 4;
143	members(0, 1, 2, 3);
144	}
145	}
146
147	molecule{
148	name = "TIP5P";
149	nAtoms = 5;
150	atom[0]{
151	type = "O_TIP5P";
152	position( 0.0, 0.0, -0.06556 );
153	}
154	atom[1]{
155	type = "H_TIP5P";
156	position( 0.0, 0.75695, 0.52032 );
157	}
158	atom[2]{
159	type = "H_TIP5P";
160	position( 0.0, -0.75695, 0.52032 );
161	}
162	atom[3]{
163	type = "EP_TIP5P";
164	position( 0.57154, 0.0, -0.46971 );
165	}
166	atom[4]{
167	type = "EP_TIP5P";
168	position( -0.57154, 0.0, -0.46971 );
169	}
170	nRigidBodies = 1;
171	rigidBody[0]{
172	nMembers = 5;
173	members(0, 1, 2, 3, 4);
174	}
175
176	nCutoffGroups = 1;
177	cutoffGroup[0]{
178	nMembers = 5;
179	members(0, 1, 2, 3, 4);
180	}
181	}
182
183	molecule{
184	name = "SPCE";
185	nAtoms = 3;
186	atom[0]{
187	type = "O_SPCE";
188	position( 0.0, 0.0, -0.06461 );
189	}
190	atom[1]{
191	type = "H_SPCE";
192	position( 0.0, 0.81649, 0.51275 );
193	}
194	atom[2]{
195	type = "H_SPCE";
196	position( 0.0, -0.81649, 0.51275 );
197	}
198	nRigidBodies = 1;
199	rigidBody[0]{
200	nMembers = 3;
201	members(0, 1, 2);
202	}
203
204	nCutoffGroups = 1;
205	cutoffGroup[0]{
206	nMembers = 3;
207	members(0, 1, 2);
208	}
209	}
210
211	molecule{
212	name = "SPC";
213	nAtoms = 3;
214	atom[0]{
215	type = "O_SPC";
216	position( 0.0, 0.0, -0.06461 );
217	}
218	atom[1]{
219	type = "H_SPC";
220	position( 0.0, 0.81649, 0.51275 );
221	}
222	atom[2]{
223	type = "H_SPC";
224	position( 0.0, -0.81649, 0.51275 );
225	}
226	nRigidBodies = 1;
227	rigidBody[0]{
228	nMembers = 3;
229	members(0, 1, 2);
230	}
231
232	nCutoffGroups = 1;
233	cutoffGroup[0]{
234	nMembers = 3;
235	members(0, 1, 2);
236	}
237	}
238
239	molecule{
240	name = "DPD";
241	nAtoms = 1;
242	atom[0]{
243	type = "DPD";
244	position(0.0, 0.0, 0.0);
245	}
246	}
247
248	#endif