3 |
|
|
4 |
|
molecule{ |
5 |
|
name = "Cl-"; |
6 |
< |
nAtoms = 1; |
6 |
> |
|
7 |
|
atom[0]{ |
8 |
|
type = "Cl-"; |
9 |
|
position(0.0, 0.0, 0.0); |
12 |
|
|
13 |
|
molecule{ |
14 |
|
name = "Na+"; |
15 |
< |
nAtoms = 1; |
15 |
> |
|
16 |
|
atom[0]{ |
17 |
< |
type = "Na"; |
17 |
> |
type = "Na+"; |
18 |
|
position(0.0, 0.0, 0.0); |
19 |
|
} |
20 |
|
} |
21 |
|
|
22 |
|
molecule{ |
23 |
|
name = "SSD_E"; |
24 |
< |
nAtoms = 1; |
24 |
> |
|
25 |
|
atom[0]{ |
26 |
|
type = "SSD_E"; |
27 |
|
position( 0.0, 0.0, 0.0 ); |
31 |
|
|
32 |
|
molecule{ |
33 |
|
name = "SSD_RF"; |
34 |
< |
nAtoms = 1; |
34 |
> |
|
35 |
|
atom[0]{ |
36 |
|
type = "SSD_RF"; |
37 |
|
position( 0.0, 0.0, 0.0 ); |
41 |
|
|
42 |
|
molecule{ |
43 |
|
name = "SSD"; |
44 |
< |
nAtoms = 1; |
44 |
> |
|
45 |
|
atom[0]{ |
46 |
|
type = "SSD"; |
47 |
|
position( 0.0, 0.0, 0.0 ); |
51 |
|
|
52 |
|
molecule{ |
53 |
|
name = "SSD1"; |
54 |
< |
nAtoms = 1; |
54 |
> |
|
55 |
|
atom[0]{ |
56 |
|
type = "SSD1"; |
57 |
|
position( 0.0, 0.0, 0.0 ); |
60 |
|
} |
61 |
|
|
62 |
|
molecule{ |
63 |
< |
name = "TAP"; |
64 |
< |
nAtoms = 1; |
63 |
> |
name = "TRED"; |
64 |
> |
|
65 |
|
atom[0]{ |
66 |
< |
type = "TAP"; |
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 |
+ |
cutoffGroup{ |
80 |
+ |
members(0, 1); |
81 |
+ |
} |
82 |
|
} |
83 |
|
|
84 |
|
molecule{ |
85 |
|
name = "TIP3P"; |
86 |
< |
nAtoms = 3; |
86 |
> |
|
87 |
|
atom[0]{ |
88 |
|
type = "O_TIP3P"; |
89 |
|
position( 0.0, 0.0, -0.06556 ); |
97 |
|
position( 0.0, -0.75695, 0.52032 ); |
98 |
|
} |
99 |
|
|
100 |
< |
nRigidBodies = 1; |
100 |
> |
|
101 |
|
rigidBody[0]{ |
102 |
< |
nMembers = 3; |
102 |
> |
|
103 |
|
members(0, 1, 2); |
104 |
|
} |
105 |
|
|
106 |
< |
nCutoffGroups = 1; |
107 |
< |
cutoffGroup[0]{ |
108 |
< |
nMembers = 3; |
106 |
> |
|
107 |
> |
cutoffGroup{ |
108 |
> |
|
109 |
|
members(0, 1, 2); |
110 |
|
} |
111 |
|
} |
112 |
|
|
113 |
|
molecule{ |
114 |
|
name = "TIP4P"; |
115 |
< |
nAtoms = 4; |
115 |
> |
|
116 |
|
atom[0]{ |
117 |
|
type = "O_TIP4P"; |
118 |
|
position( 0.0, 0.0, -0.06556 ); |
129 |
|
type = "EP_TIP4P"; |
130 |
|
position( 0.0, 0.0, 0.08444 ); |
131 |
|
} |
132 |
< |
nRigidBodies = 1; |
132 |
> |
|
133 |
|
rigidBody[0]{ |
134 |
< |
nMembers = 4; |
134 |
> |
|
135 |
|
members(0, 1, 2, 3); |
136 |
|
} |
137 |
|
|
138 |
< |
nCutoffGroups = 1; |
139 |
< |
cutoffGroup[0]{ |
140 |
< |
nMembers = 4; |
138 |
> |
|
139 |
> |
cutoffGroup{ |
140 |
> |
|
141 |
|
members(0, 1, 2, 3); |
142 |
|
} |
143 |
|
} |
144 |
|
|
145 |
|
molecule{ |
146 |
+ |
name = "TIP4P-Ew"; |
147 |
+ |
|
148 |
+ |
atom[0]{ |
149 |
+ |
type = "O_TIP4P-Ew"; |
150 |
+ |
position( 0.0, 0.0, -0.06556 ); |
151 |
+ |
} |
152 |
+ |
atom[1]{ |
153 |
+ |
type = "H_TIP4P-Ew"; |
154 |
+ |
position( 0.0, 0.75695, 0.52032 ); |
155 |
+ |
} |
156 |
+ |
atom[2]{ |
157 |
+ |
type = "H_TIP4P-Ew"; |
158 |
+ |
position( 0.0, -0.75695, 0.52032 ); |
159 |
+ |
} |
160 |
+ |
atom[3]{ |
161 |
+ |
type = "EP_TIP4P-Ew"; |
162 |
+ |
position( 0.0, 0.0, 0.05944 ); |
163 |
+ |
} |
164 |
+ |
|
165 |
+ |
rigidBody[0]{ |
166 |
+ |
|
167 |
+ |
members(0, 1, 2, 3); |
168 |
+ |
} |
169 |
+ |
|
170 |
+ |
|
171 |
+ |
cutoffGroup{ |
172 |
+ |
|
173 |
+ |
members(0, 1, 2, 3); |
174 |
+ |
} |
175 |
+ |
} |
176 |
+ |
|
177 |
+ |
molecule{ |
178 |
|
name = "TIP5P"; |
179 |
< |
nAtoms = 5; |
179 |
> |
|
180 |
|
atom[0]{ |
181 |
|
type = "O_TIP5P"; |
182 |
|
position( 0.0, 0.0, -0.06556 ); |
197 |
|
type = "EP_TIP5P"; |
198 |
|
position( -0.57154, 0.0, -0.46971 ); |
199 |
|
} |
200 |
< |
nRigidBodies = 1; |
200 |
> |
|
201 |
|
rigidBody[0]{ |
202 |
< |
nMembers = 5; |
202 |
> |
|
203 |
|
members(0, 1, 2, 3, 4); |
204 |
|
} |
205 |
|
|
206 |
< |
nCutoffGroups = 1; |
207 |
< |
cutoffGroup[0]{ |
208 |
< |
nMembers = 5; |
206 |
> |
|
207 |
> |
cutoffGroup{ |
208 |
> |
|
209 |
|
members(0, 1, 2, 3, 4); |
210 |
|
} |
211 |
|
} |
212 |
|
|
213 |
|
molecule{ |
214 |
+ |
name = "TIP5P-E"; |
215 |
+ |
|
216 |
+ |
atom[0]{ |
217 |
+ |
type = "O_TIP5P-E"; |
218 |
+ |
position( 0.0, 0.0, -0.06556 ); |
219 |
+ |
} |
220 |
+ |
atom[1]{ |
221 |
+ |
type = "H_TIP5P"; |
222 |
+ |
position( 0.0, 0.75695, 0.52032 ); |
223 |
+ |
} |
224 |
+ |
atom[2]{ |
225 |
+ |
type = "H_TIP5P"; |
226 |
+ |
position( 0.0, -0.75695, 0.52032 ); |
227 |
+ |
} |
228 |
+ |
atom[3]{ |
229 |
+ |
type = "EP_TIP5P"; |
230 |
+ |
position( 0.57154, 0.0, -0.46971 ); |
231 |
+ |
} |
232 |
+ |
atom[4]{ |
233 |
+ |
type = "EP_TIP5P"; |
234 |
+ |
position( -0.57154, 0.0, -0.46971 ); |
235 |
+ |
} |
236 |
+ |
|
237 |
+ |
rigidBody[0]{ |
238 |
+ |
|
239 |
+ |
members(0, 1, 2, 3, 4); |
240 |
+ |
} |
241 |
+ |
|
242 |
+ |
|
243 |
+ |
cutoffGroup{ |
244 |
+ |
|
245 |
+ |
members(0, 1, 2, 3, 4); |
246 |
+ |
} |
247 |
+ |
} |
248 |
+ |
|
249 |
+ |
molecule{ |
250 |
|
name = "SPCE"; |
251 |
< |
nAtoms = 3; |
251 |
> |
|
252 |
|
atom[0]{ |
253 |
|
type = "O_SPCE"; |
254 |
|
position( 0.0, 0.0, -0.06461 ); |
261 |
|
type = "H_SPCE"; |
262 |
|
position( 0.0, -0.81649, 0.51275 ); |
263 |
|
} |
264 |
< |
nRigidBodies = 1; |
264 |
> |
|
265 |
|
rigidBody[0]{ |
266 |
< |
nMembers = 3; |
266 |
> |
|
267 |
|
members(0, 1, 2); |
268 |
|
} |
269 |
|
|
270 |
< |
nCutoffGroups = 1; |
271 |
< |
cutoffGroup[0]{ |
272 |
< |
nMembers = 3; |
270 |
> |
|
271 |
> |
cutoffGroup{ |
272 |
> |
|
273 |
|
members(0, 1, 2); |
274 |
|
} |
275 |
+ |
} |
276 |
|
|
277 |
+ |
molecule{ |
278 |
+ |
name = "SPC"; |
279 |
+ |
|
280 |
+ |
atom[0]{ |
281 |
+ |
type = "O_SPC"; |
282 |
+ |
position( 0.0, 0.0, -0.06461 ); |
283 |
+ |
} |
284 |
+ |
atom[1]{ |
285 |
+ |
type = "H_SPC"; |
286 |
+ |
position( 0.0, 0.81649, 0.51275 ); |
287 |
+ |
} |
288 |
+ |
atom[2]{ |
289 |
+ |
type = "H_SPC"; |
290 |
+ |
position( 0.0, -0.81649, 0.51275 ); |
291 |
+ |
} |
292 |
+ |
|
293 |
+ |
rigidBody[0]{ |
294 |
+ |
|
295 |
+ |
members(0, 1, 2); |
296 |
+ |
} |
297 |
+ |
|
298 |
+ |
|
299 |
+ |
cutoffGroup{ |
300 |
+ |
|
301 |
+ |
members(0, 1, 2); |
302 |
+ |
} |
303 |
|
} |
304 |
|
|
305 |
|
molecule{ |
306 |
|
name = "DPD"; |
307 |
< |
nAtoms = 1; |
307 |
> |
|
308 |
|
atom[0]{ |
309 |
|
type = "DPD"; |
310 |
|
position(0.0, 0.0, 0.0); |