samples/lipid/lipid.md

molecule{
  
  name = "simpleLipid_16";
  

  atom[0]{
    type = "HEAD";
    position( 0.0, 1.01479, 0.65901 );
    orientation( 0.0, 0.0, 0.0 );
  }
  atom[1]{
    type = "CH2";
    position( 0.0, -0.8387, -1.292 );
  }
  atom[2]{
    type = "CH2";
    position( 0.0, 0.0, -2.584 );
  }
  atom[3]{
    type = "CH2";
    position( 0.0, -0.8387, -3.876 );
  }
  atom[4]{
    type = "CH2";
    position( 0.0, 0.0, -5.168 );
  }
  atom[5]{
    type = "CH2";
    position( 0.0, -0.8387, -6.46 );
  }
  atom[6]{
    type = "CH2";
    position( 0.0, 0.0, -7.752 );
  }
  atom[7]{
    type = "CH2";
    position( 0.0, -0.8387, -9.044 );
  }
  atom[8]{
    type = "CH2";
    position( 0.0, 0.0, -10.336 );
  }
  atom[9]{
    type = "CH2";
    position( 0.0, -0.8387, -11.628 );
  }
  atom[10]{
    type = "CH2";
    position( 0.0, 0.0, -12.92 );
  }
  atom[11]{
    type = "CH2";
    position( 0.0, -0.8387, -14.212 );
  }
  atom[12]{
    type = "CH2";
    position( 0.0, 0.0, -15.504 );
  }
  atom[13]{
    type = "CH2";
    position( 0.0, -0.8387, -16.796 );
  }
  atom[14]{
    type = "CH2";
    position( 0.0, 0.0, -18.08 );
  }
  atom[15]{
    type = "CH2";
    position( 0.0, -0.8387, -19.38 );
  }
  atom[16]{
    type = "CH3";
    position( 0.0, 0.0, -20.672 );
  }

  
  bond{
    members( 0, 1 );
  }
  bond{
    members( 1, 2 );
  }
  bond{
    members( 2, 3 );
  }
  bond{
    members( 3, 4 );
  }
  bond{
    members( 4, 5 );
  }
  bond{
    members( 5, 6 );
  }
  bond{
    members( 6, 7 );
  }
  bond{
    members( 7, 8 );
  }
  bond{
    members( 8, 9 );
  }
  bond{
    members( 9, 10 );
  }
  bond{
    members( 10, 11 );
  }
  bond{
    members( 11, 12 );
  }
  bond{
    members( 12, 13 );
  }
  bond{
    members( 13, 14 );
  }
  bond{
    members( 14, 15 );
  }
  bond{
    members( 15, 16 );
  }

  
  bend{
    members( 0, 1, 2 );
  }
  bend{
    members( 1, 2, 3 );
  }
  bend{
    members( 2, 3, 4 );
  }
  bend{
    members( 3, 4, 5 );
  }
  bend{
    members( 4, 5, 6 );
  }
  bend{
    members( 5, 6, 7 );
  }
  bend{
    members( 6, 7, 8 );
  }
  bend{
    members( 7, 8, 9 );
  }
  bend{
    members( 8, 9, 10 );
  }
  bend{
    members( 9, 10, 11 );
  }
  bend{
    members( 10, 11, 12 );
  }
  bend{
    members( 11, 12, 13 );
  }
  bend{
    members( 12, 13, 14 );
  }
  bend{
    members( 13, 14, 15 );
  }
  bend{
    members( 14, 15, 16 );
  }

  
  torsion{
    members( 0, 1, 2, 3 );
  }
  torsion{
    members( 1, 2, 3, 4 );
  }
  torsion{
    members( 2, 3, 4, 5 );
  }
  torsion{
    members( 3, 4, 5, 6 );
  }
  torsion{
    members( 4, 5, 6, 7 );
  }
  torsion{
    members( 5, 6, 7, 8 );
  }
  torsion{
    members( 6, 7, 8, 9 );
  }
  torsion{
    members( 7, 8, 9, 10 );
  }
  torsion{
    members( 8, 9, 10, 11 );
  }
  torsion{
    members( 9, 10, 11, 12 );
  }
  torsion{
    members( 10, 11, 12, 13 );
  }
  torsion{
    members( 11, 12, 13, 14 );
  }
  torsion{
    members( 12, 13, 14, 15 );
  }
  torsion{
    members( 13, 14, 15, 16 );
  }
}

molecule{
  
  name = "simpleLipid_16G";
  

  atom[0]{
    type = "HEAD";
    position( 0.0, 1.01479, 0.65901 );
    orientation( 0.0, 0.0, 0.0 );
  }
  atom[1]{
    type = "CH2";
    position( 0.0, -0.8387, -1.292 );
  }
  atom[2]{
    type = "CH2";
    position( 0.0, 0.0, -2.584 );
  }
  atom[3]{
    type = "CH2";
    position( 0.0, -0.8387, -3.876 );
  }
  atom[4]{
    type = "CH2";
    position( 0.0, 0.0, -5.168 );
  }
  atom[5]{
    type = "CH2";
    position( 0.0, -0.8387, -6.46 );
  }
  atom[6]{
    type = "CH2";
    position( 0.0, 0.0, -7.752 );
  }
  atom[7]{
    type = "CH2";
    position( 0.0, -0.8387, -9.044 );
  }
  atom[8]{
    type = "CH2";
    position( 0.0, 0.0, -10.336 );
  }
  atom[9]{
    type = "CH2";
    position( 0.0, -0.8387, -11.628 );
  }
  atom[10]{
    type = "CH2";
    position( 0.0, 0.0, -12.92 );
  }
  atom[11]{
    type = "CH2";
    position( 0.0, -0.8387, -14.212 );
  }
  atom[12]{
    type = "CH2";
    position( 0.0, 0.0, -15.504 );
  }
  atom[13]{
    type = "CH2";
    position( 0.0, -0.8387, -16.796 );
  }
  atom[14]{
    type = "CH2";
    position( 0.0, 0.0, -18.08 );
  }
  atom[15]{
    type = "CH2";
    position( 0.0, -0.8387, -19.38 );
  }
  atom[16]{
    type = "CH3";
    position( 0.0, 0.0, -20.672 );
  }

  
  bond{
    members( 0, 1 );
  }
  bond{
    members( 1, 2 );
  }
  bond{
    members( 2, 3 );
  }
  bond{
    members( 3, 4 );
  }
  bond{
    members( 4, 5 );
  }
  bond{
    members( 5, 6 );
  }
  bond{
    members( 6, 7 );
  }
  bond{
    members( 7, 8 );
  }
  bond{
    members( 8, 9 );
  }
  bond{
    members( 9, 10 );
  }
  bond{
    members( 10, 11 );
  }
  bond{
    members( 11, 12 );
  }
  bond{
    members( 12, 13 );
  }
  bond{
    members( 13, 14 );
  }
  bond{
    members( 14, 15 );
  }
  bond{
    members( 15, 16 );
  }

  
  bend{
    members( 0, 1, 2 );
  }
  bend{
    members( 1, 2, 3 );
  }
  bend{
    members( 2, 3, 4 );
  }
  bend{
    members( 3, 4, 5 );
  }
  bend{
    members( 4, 5, 6 );
  }
  bend{
    members( 5, 6, 7 );
  }
  bend{
    members( 6, 7, 8 );
  }
  bend{
    members( 7, 8, 9 );
  }
  bend{
    members( 8, 9, 10 );
  }
  bend{
    members( 9, 10, 11 );
  }
  bend{
    members( 10, 11, 12 );
  }
  bend{
    members( 11, 12, 13 );
  }
  bend{
    members( 12, 13, 14 );
  }
  bend{
    members( 13, 14, 15 );
  }
  bend{
    members( 14, 15, 16 );
  }
  bend{
    members( 0, 1 );
    ghostVectorSource = 0;
  }


  torsion{
    members( 0, 1, 2, 3 );
  }
  torsion{
    members( 1, 2, 3, 4 );
  }
  torsion{
    members( 2, 3, 4, 5 );
  }
  torsion{
    members( 3, 4, 5, 6 );
  }
  torsion{
    members( 4, 5, 6, 7 );
  }
  torsion{
    members( 5, 6, 7, 8 );
  }
  torsion{
    members( 6, 7, 8, 9 );
  }
  torsion{
    members( 7, 8, 9, 10 );
  }
  torsion{
    members( 8, 9, 10, 11 );
  }
  torsion{
    members( 9, 10, 11, 12 );
  }
  torsion{
    members( 10, 11, 12, 13 );
  }
  torsion{
    members( 11, 12, 13, 14 );
  }
  torsion{
    members( 12, 13, 14, 15 );
  }
  torsion{
    members( 13, 14, 15, 16 );
  }
}

molecule{
  
  name = "twoChain_14G";
  

  atom[0]{
    type = "HEAD";
    position( -0.110050, 1.249033, -0.023976 );
    orientation( 0.0, 0.0, 0.0 );
  }
  atom[1]{
    type = "CH2";
    position( 0.784436, -1.064213, -1.211953 );
  }
  atom[2]{
    type = "CH";
    position( 1.109791, -0.911911, -2.709467 );
  }
  atom[3]{
    type = "CH2";
    position( -0.268917, -0.607952, -3.324586 );
  }
  atom[4]{
    type = "CH2";
    position( -0.331805, 0.044474, -4.718138 );
  }
  atom[5]{
    type = "CH2";
    position( -0.103214, -0.867134, -5.938104 );
  }
  atom[6]{
    type = "CH2";
    position( -0.181619, -0.100307, -7.271307 );
  }
  atom[7]{
    type = "CH2";
    position( 0.042505, -0.939979, -8.542653 );
  }
  atom[8]{
    type = "CH2";
    position( -0.051368, -0.117766, -9.841404 );
  }
  atom[9]{
    type = "CH2";
    position( 0.142860, -0.925076, -11.138372 );
  }
  atom[10]{
    type = "CH2";
    position( 0.019593, -0.083625, -12.422259 );
  }
  atom[11]{
    type = "CH2";
    position( 0.180051, -0.885777, -13.727022 );
  }
  atom[12]{
    type = "CH2";
    position( 0.034763, -0.043486, -15.008052 );
  }
  atom[13]{
    type = "CH2";
    position( 0.173235, -0.851987, -16.311414);
  }
  atom[14]{
    type = "CH2";
    position( 0.018726, -0.013912, -17.594129);
  }
  atom[15]{
    type = "CH2";
    position( 0.148780, -0.828559, -18.894528 );
  }
  atom[16]{
    type = "CH3";
    position( -0.005954, 0.007456, -20.178559 );
  }
  atom[17]{
    type = "CH2";
    position( 2.634030, -1.130837, -2.728703);
  }
  atom[18]{
    type = "CH2";
    position( 3.297380, -1.543544, -4.055820 );
  }
  atom[19]{
    type = "CH2";
    position( 3.457273, -0.451637, -5.129958 );
  }
  atom[20]{
    type = "CH2";
    position( 4.094249, -1.019043, -6.412110 );
  }
  atom[21]{
    type = "CH2";
    position( 4.235779, -0.046073, -7.597395 );
  }
  atom[22]{
    type = "CH2";
    position( 4.820154, -0.745979, -8.838458 );
  }
  atom[23]{
    type = "CH2";
    position( 4.932879, 0.124112, -10.104093 );
  }
  atom[24]{
    type = "CH2";
    position( 5.429202, -0.669482, -11.326988 );
  }
  atom[25]{
    type = "CH2";
    position( 5.471807, 0.135950, -12.638881 );
  }
  atom[26]{
    type = "CH2";
    position( 5.843335, -0.710717, -13.870434 );
  }
  atom[27]{
    type = "CH2";
    position( 5.795449, 0.066888, -15.198830 );
  }
  atom[28]{
    type = "CH2";
    position( 6.056385, -0.801301, -16.443724 );
  }
  atom[29]{
    type = "CH2";
    position( 5.952060, -0.029856, -17.772479 );
  }
  atom[30]{
    type = "CH3";
    position( 6.164077, -0.903155, -19.023077 );
  }

  
  bond{
    members( 0, 1 );
  }
  bond{
    members( 1, 2 );
  }
  bond{
    members( 2, 3 );
  }
  bond{
    members( 3, 4 );
  }
  bond{
    members( 4, 5 );
  }
  bond{
    members( 5, 6 );
  }
  bond{
    members( 6, 7 );
  }
  bond{
    members( 7, 8 );
  }
  bond{
    members( 8, 9 );
  }
  bond{
    members( 9, 10 );
  }
  bond{
    members( 10, 11 );
  }
  bond{
    members( 11, 12 );
  }
  bond{
    members( 12, 13 );
  }
  bond{
    members( 13, 14 );
  }
  bond{
    members( 14, 15 );
  }
  bond{
    members( 15, 16 );
  }
  bond{
    members( 2, 17 );
  }
  bond{
    members( 17, 18 );
  }
  bond{
    members( 18, 19 );
  }
  bond{
    members( 19, 20 );
  }
  bond{
    members( 20, 21 );
  }
  bond{
    members( 21, 22 );
  }
  bond{
    members( 22, 23 );
  }
  bond{
    members( 23, 24 );
  }
  bond{
    members( 24, 25 );
  }
  bond{
    members( 25, 26 );
  }
  bond{
    members( 26, 27 );
  }
  bond{
    members( 27, 28 );
  }
  bond{
    members( 28, 29 );
  }
  bond{
    members( 29, 30 );
  }

  
  bend{
    members( 0, 1, 2 );
  }
  bend{
    members( 1, 2, 3 );
  }
  bend{
    members( 2, 3, 4 );
  }
  bend{
    members( 3, 4, 5 );
  }
  bend{
    members( 4, 5, 6 );
  }
  bend{
    members( 5, 6, 7 );
  }
  bend{
    members( 6, 7, 8 );
  }
  bend{
    members( 7, 8, 9 );
  }
  bend{
    members( 8, 9, 10 );
  }
  bend{
    members( 9, 10, 11 );
  }
  bend{
    members( 10, 11, 12 );
  }
  bend{
    members( 11, 12, 13 );
  }
  bend{
    members( 12, 13, 14 );
  }
  bend{
    members( 13, 14, 15 );
  }
  bend{
    members( 14, 15, 16 );
  }
  bend{
    members( 0, 1 );
    ghostVectorSource = 0;
  }
  bend{
    members( 1, 2, 17 );
  }
  bend{
    members( 2, 17, 18 );
  }
  bend{
    members( 17, 18, 19 );
  }
  bend{
    members( 18, 19, 20 );
  }
  bend{
    members( 19, 20, 21 );
  }
  bend{
    members( 20, 21, 22 );
  }
  bend{
    members( 21, 22, 23 );
  }
  bend{
    members( 22, 23, 24 );
  }
  bend{
    members( 23, 24, 25 );
  }
  bend{
    members( 24, 25, 26 );
  }
  bend{
    members( 25, 26, 27 );
  }
  bend{
    members( 26, 27, 28 );
  }
  bend{
    members( 27, 28, 29 );
  }
  bend{
    members( 28, 29, 30 );
  }


  torsion{
    members( 0, 1, 2, 3 );
  }
  torsion{
    members( 1, 2, 3, 4 );
  }
  torsion{
    members( 2, 3, 4, 5 );
  }
  torsion{
    members( 3, 4, 5, 6 );
  }
  torsion{
    members( 4, 5, 6, 7 );
  }
  torsion{
    members( 5, 6, 7, 8 );
  }
  torsion{
    members( 6, 7, 8, 9 );
  }
  torsion{
    members( 7, 8, 9, 10 );
  }
  torsion{
    members( 8, 9, 10, 11 );
  }
  torsion{
    members( 9, 10, 11, 12 );
  }
  torsion{
    members( 10, 11, 12, 13 );
  }
  torsion{
    members( 11, 12, 13, 14 );
  }
  torsion{
    members( 12, 13, 14, 15 );
  }
  torsion{
    members( 13, 14, 15, 16 );
  }
  torsion{
    members( 1, 2, 17, 18 );
  }
  torsion{
    members( 2, 17, 18, 19 );
  }
  torsion{
    members( 17, 18, 19, 20 );
  }
  torsion{
    members( 18, 19, 20, 21 );
  }
  torsion{
    members( 19, 20, 21, 22 );
  }
  torsion{
    members( 20, 21, 22, 23 );
  }
  torsion{
    members( 21, 22, 23, 24 );
  }
  torsion{
    members( 22, 23, 24, 25 );
  }
  torsion{
    members( 23, 24, 25, 26 );
  }
  torsion{
    members( 24, 25, 26, 27 );
  }
  torsion{
    members( 25, 26, 27, 28 );
  }
  torsion{
    members( 26, 27, 28, 29 );
  }
  torsion{
    members( 27, 28, 29, 30 );
  }

}
Revision:	2489
Committed:	Tue Dec 6 16:49:59 2005 UTC (18 years, 7 months ago) by tim
File size:	12089 byte(s)
Log Message:	remove deprecated keywords from samples
#	Content
1	molecule{
2
3	name = "simpleLipid_16";
4
5
6	atom[0]{
7	type = "HEAD";
8	position( 0.0, 1.01479, 0.65901 );
9	orientation( 0.0, 0.0, 0.0 );
10	}
11	atom[1]{
12	type = "CH2";
13	position( 0.0, -0.8387, -1.292 );
14	}
15	atom[2]{
16	type = "CH2";
17	position( 0.0, 0.0, -2.584 );
18	}
19	atom[3]{
20	type = "CH2";
21	position( 0.0, -0.8387, -3.876 );
22	}
23	atom[4]{
24	type = "CH2";
25	position( 0.0, 0.0, -5.168 );
26	}
27	atom[5]{
28	type = "CH2";
29	position( 0.0, -0.8387, -6.46 );
30	}
31	atom[6]{
32	type = "CH2";
33	position( 0.0, 0.0, -7.752 );
34	}
35	atom[7]{
36	type = "CH2";
37	position( 0.0, -0.8387, -9.044 );
38	}
39	atom[8]{
40	type = "CH2";
41	position( 0.0, 0.0, -10.336 );
42	}
43	atom[9]{
44	type = "CH2";
45	position( 0.0, -0.8387, -11.628 );
46	}
47	atom[10]{
48	type = "CH2";
49	position( 0.0, 0.0, -12.92 );
50	}
51	atom[11]{
52	type = "CH2";
53	position( 0.0, -0.8387, -14.212 );
54	}
55	atom[12]{
56	type = "CH2";
57	position( 0.0, 0.0, -15.504 );
58	}
59	atom[13]{
60	type = "CH2";
61	position( 0.0, -0.8387, -16.796 );
62	}
63	atom[14]{
64	type = "CH2";
65	position( 0.0, 0.0, -18.08 );
66	}
67	atom[15]{
68	type = "CH2";
69	position( 0.0, -0.8387, -19.38 );
70	}
71	atom[16]{
72	type = "CH3";
73	position( 0.0, 0.0, -20.672 );
74	}
75
76
77
78	bond{
79	members( 0, 1 );
80	}
81	bond{
82	members( 1, 2 );
83	}
84	bond{
85	members( 2, 3 );
86	}
87	bond{
88	members( 3, 4 );
89	}
90	bond{
91	members( 4, 5 );
92	}
93	bond{
94	members( 5, 6 );
95	}
96	bond{
97	members( 6, 7 );
98	}
99	bond{
100	members( 7, 8 );
101	}
102	bond{
103	members( 8, 9 );
104	}
105	bond{
106	members( 9, 10 );
107	}
108	bond{
109	members( 10, 11 );
110	}
111	bond{
112	members( 11, 12 );
113	}
114	bond{
115	members( 12, 13 );
116	}
117	bond{
118	members( 13, 14 );
119	}
120	bond{
121	members( 14, 15 );
122	}
123	bond{
124	members( 15, 16 );
125	}
126
127
128
129	bend{
130	members( 0, 1, 2 );
131	}
132	bend{
133	members( 1, 2, 3 );
134	}
135	bend{
136	members( 2, 3, 4 );
137	}
138	bend{
139	members( 3, 4, 5 );
140	}
141	bend{
142	members( 4, 5, 6 );
143	}
144	bend{
145	members( 5, 6, 7 );
146	}
147	bend{
148	members( 6, 7, 8 );
149	}
150	bend{
151	members( 7, 8, 9 );
152	}
153	bend{
154	members( 8, 9, 10 );
155	}
156	bend{
157	members( 9, 10, 11 );
158	}
159	bend{
160	members( 10, 11, 12 );
161	}
162	bend{
163	members( 11, 12, 13 );
164	}
165	bend{
166	members( 12, 13, 14 );
167	}
168	bend{
169	members( 13, 14, 15 );
170	}
171	bend{
172	members( 14, 15, 16 );
173	}
174
175
176
177	torsion{
178	members( 0, 1, 2, 3 );
179	}
180	torsion{
181	members( 1, 2, 3, 4 );
182	}
183	torsion{
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215	}
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218	}
219	}
220
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222
223	name = "simpleLipid_16G";
224
225
226	atom[0]{
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229	orientation( 0.0, 0.0, 0.0 );
230	}
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234	}
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238	}
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275	atom[12]{
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278	}
279	atom[13]{
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282	}
283	atom[14]{
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286	}
287	atom[15]{
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290	}
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294	}
295
296
297
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347
348
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398
399
400
401
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450
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576
577
578
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670
671
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764
765
766
767
768
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850
851	}