samples/lipid/water.md

#ifndef _WATER_MD_
#define _WATER_MD_

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

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

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

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

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

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

molecule{
  name = "TRED";
  
  atom[0]{
    type = "TRED";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
  atom[1]{
    type = "EP_TRED";
    position( 0.0, 0.0, 0.5 );
  }

  rigidBody[0]{
    members(0, 1);
  }
}

molecule{
  name = "TIP3P";
  
  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 );
  }
  
  rigidBody[0]{     
    members(0, 1, 2);
  }  
}

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

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

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

molecule{
  name = "TIP5P-E";
  
  atom[0]{
    type = "O_TIP5P-E";
    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 );
  }
  
  rigidBody[0]{    
    members(0, 1, 2, 3, 4);
  }
}

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

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

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

#endif
Revision:	1393
Committed:	Wed Nov 25 20:36:46 2009 UTC (15 years, 11 months ago) by gezelter
File size:	3749 byte(s)
Log Message:	removing spurious cutoffGroup lines from default water.md sample files
#	Content
1	#ifndef _WATER_MD_
2	#define _WATER_MD_
3
4	molecule{
5	name = "Cl-";
6
7	atom[0]{
8	type = "Cl-";
9	position(0.0, 0.0, 0.0);
10	}
11	}
12
13	molecule{
14	name = "Na+";
15
16	atom[0]{
17	type = "Na+";
18	position(0.0, 0.0, 0.0);
19	}
20	}
21
22	molecule{
23	name = "SSD_E";
24
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
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
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
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 = "TRED";
64
65	atom[0]{
66	type = "TRED";
67	position( 0.0, 0.0, 0.0 );
68	orientation( 0.0, 0.0, 0.0 );
69	}
70	atom[1]{
71	type = "EP_TRED";
72	position( 0.0, 0.0, 0.5 );
73	}
74
75	rigidBody[0]{
76	members(0, 1);
77	}
78	}
79
80	molecule{
81	name = "TIP3P";
82
83	atom[0]{
84	type = "O_TIP3P";
85	position( 0.0, 0.0, -0.06556 );
86	}
87	atom[1]{
88	type = "H_TIP3P";
89	position( 0.0, 0.75695, 0.52032 );
90	}
91	atom[2]{
92	type = "H_TIP3P";
93	position( 0.0, -0.75695, 0.52032 );
94	}
95
96	rigidBody[0]{
97	members(0, 1, 2);
98	}
99	}
100
101	molecule{
102	name = "TIP4P";
103
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
121	rigidBody[0]{
122	members(0, 1, 2, 3);
123	}
124	}
125
126	molecule{
127	name = "TIP4P-Ew";
128
129	atom[0]{
130	type = "O_TIP4P-Ew";
131	position( 0.0, 0.0, -0.06556 );
132	}
133	atom[1]{
134	type = "H_TIP4P-Ew";
135	position( 0.0, 0.75695, 0.52032 );
136	}
137	atom[2]{
138	type = "H_TIP4P-Ew";
139	position( 0.0, -0.75695, 0.52032 );
140	}
141	atom[3]{
142	type = "EP_TIP4P-Ew";
143	position( 0.0, 0.0, 0.05944 );
144	}
145
146	rigidBody[0]{
147	members(0, 1, 2, 3);
148	}
149	}
150
151	molecule{
152	name = "TIP5P";
153
154	atom[0]{
155	type = "O_TIP5P";
156	position( 0.0, 0.0, -0.06556 );
157	}
158	atom[1]{
159	type = "H_TIP5P";
160	position( 0.0, 0.75695, 0.52032 );
161	}
162	atom[2]{
163	type = "H_TIP5P";
164	position( 0.0, -0.75695, 0.52032 );
165	}
166	atom[3]{
167	type = "EP_TIP5P";
168	position( 0.57154, 0.0, -0.46971 );
169	}
170	atom[4]{
171	type = "EP_TIP5P";
172	position( -0.57154, 0.0, -0.46971 );
173	}
174
175	rigidBody[0]{
176	members(0, 1, 2, 3, 4);
177	}
178	}
179
180	molecule{
181	name = "TIP5P-E";
182
183	atom[0]{
184	type = "O_TIP5P-E";
185	position( 0.0, 0.0, -0.06556 );
186	}
187	atom[1]{
188	type = "H_TIP5P";
189	position( 0.0, 0.75695, 0.52032 );
190	}
191	atom[2]{
192	type = "H_TIP5P";
193	position( 0.0, -0.75695, 0.52032 );
194	}
195	atom[3]{
196	type = "EP_TIP5P";
197	position( 0.57154, 0.0, -0.46971 );
198	}
199	atom[4]{
200	type = "EP_TIP5P";
201	position( -0.57154, 0.0, -0.46971 );
202	}
203
204	rigidBody[0]{
205	members(0, 1, 2, 3, 4);
206	}
207	}
208
209	molecule{
210	name = "SPCE";
211
212	atom[0]{
213	type = "O_SPCE";
214	position( 0.0, 0.0, -0.06461 );
215	}
216	atom[1]{
217	type = "H_SPCE";
218	position( 0.0, 0.81649, 0.51275 );
219	}
220	atom[2]{
221	type = "H_SPCE";
222	position( 0.0, -0.81649, 0.51275 );
223	}
224
225	rigidBody[0]{
226	members(0, 1, 2);
227	}
228	}
229
230	molecule{
231	name = "SPC";
232
233	atom[0]{
234	type = "O_SPC";
235	position( 0.0, 0.0, -0.06461 );
236	}
237	atom[1]{
238	type = "H_SPC";
239	position( 0.0, 0.81649, 0.51275 );
240	}
241	atom[2]{
242	type = "H_SPC";
243	position( 0.0, -0.81649, 0.51275 );
244	}
245
246	rigidBody[0]{
247	members(0, 1, 2);
248	}
249	}
250
251	molecule{
252	name = "DPD";
253
254	atom[0]{
255	type = "DPD";
256	position(0.0, 0.0, 0.0);
257	}
258	}
259
260	#endif