water/dimer/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 = "TAP";
  nAtoms = 1;
  atom[0]{
    type = "TAP";
    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 = "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 = "DPD";
  nAtoms = 1;
  atom[0]{
    type = "DPD";
    position(0.0, 0.0, 0.0);
  }
}

#endif
Revision:	2229
Committed:	Tue May 17 22:35:01 2005 UTC (19 years, 1 month ago) by chrisfen
File size:	3069 byte(s)
Log Message:	Modifications to tap. Also correcting changes to the previous merge that were not caught
#	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 = "TAP";
64	nAtoms = 1;
65	atom[0]{
66	type = "TAP";
67	position( 0.0, 0.0, 0.0 );
68	orientation( 0.0, 0.0, 0.0 );
69	}
70	}
71
72	molecule{
73	name = "TIP3P";
74	nAtoms = 3;
75	atom[0]{
76	type = "O_TIP3P";
77	position( 0.0, 0.0, -0.06556 );
78	}
79	atom[1]{
80	type = "H_TIP3P";
81	position( 0.0, 0.75695, 0.52032 );
82	}
83	atom[2]{
84	type = "H_TIP3P";
85	position( 0.0, -0.75695, 0.52032 );
86	}
87
88	nRigidBodies = 1;
89	rigidBody[0]{
90	nMembers = 3;
91	members(0, 1, 2);
92	}
93
94	nCutoffGroups = 1;
95	cutoffGroup[0]{
96	nMembers = 3;
97	members(0, 1, 2);
98	}
99	}
100
101	molecule{
102	name = "TIP4P";
103	nAtoms = 4;
104	atom[0]{
105	type = "O_TIP4P";
106	position( 0.0, 0.0, -0.06556 );
107	}
108	atom[1]{
109	type = "H_TIP4P";
110	position( 0.0, 0.75695, 0.52032 );
111	}
112	atom[2]{
113	type = "H_TIP4P";
114	position( 0.0, -0.75695, 0.52032 );
115	}
116	atom[3]{
117	type = "EP_TIP4P";
118	position( 0.0, 0.0, 0.08444 );
119	}
120	nRigidBodies = 1;
121	rigidBody[0]{
122	nMembers = 4;
123	members(0, 1, 2, 3);
124	}
125
126	nCutoffGroups = 1;
127	cutoffGroup[0]{
128	nMembers = 4;
129	members(0, 1, 2, 3);
130	}
131	}
132
133	molecule{
134	name = "TIP5P";
135	nAtoms = 5;
136	atom[0]{
137	type = "O_TIP5P";
138	position( 0.0, 0.0, -0.06556 );
139	}
140	atom[1]{
141	type = "H_TIP5P";
142	position( 0.0, 0.75695, 0.52032 );
143	}
144	atom[2]{
145	type = "H_TIP5P";
146	position( 0.0, -0.75695, 0.52032 );
147	}
148	atom[3]{
149	type = "EP_TIP5P";
150	position( 0.57154, 0.0, -0.46971 );
151	}
152	atom[4]{
153	type = "EP_TIP5P";
154	position( -0.57154, 0.0, -0.46971 );
155	}
156	nRigidBodies = 1;
157	rigidBody[0]{
158	nMembers = 5;
159	members(0, 1, 2, 3, 4);
160	}
161
162	nCutoffGroups = 1;
163	cutoffGroup[0]{
164	nMembers = 5;
165	members(0, 1, 2, 3, 4);
166	}
167	}
168
169	molecule{
170	name = "SPCE";
171	nAtoms = 3;
172	atom[0]{
173	type = "O_SPCE";
174	position( 0.0, 0.0, -0.06461 );
175	}
176	atom[1]{
177	type = "H_SPCE";
178	position( 0.0, 0.81649, 0.51275 );
179	}
180	atom[2]{
181	type = "H_SPCE";
182	position( 0.0, -0.81649, 0.51275 );
183	}
184	nRigidBodies = 1;
185	rigidBody[0]{
186	nMembers = 3;
187	members(0, 1, 2);
188	}
189
190	nCutoffGroups = 1;
191	cutoffGroup[0]{
192	nMembers = 3;
193	members(0, 1, 2);
194	}
195
196	}
197
198	molecule{
199	name = "DPD";
200	nAtoms = 1;
201	atom[0]{
202	type = "DPD";
203	position(0.0, 0.0, 0.0);
204	}
205	}
206
207	#endif