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 = "PAIR"; |
24 |
+ |
|
25 |
+ |
atom[0]{ |
26 |
+ |
type = "Pchg+"; |
27 |
+ |
position(0.0, 1, 1.0); |
28 |
+ |
} |
29 |
+ |
atom[1]{ |
30 |
+ |
type = "Pchg+"; |
31 |
+ |
position(0.0, -1, 1.0); |
32 |
+ |
} |
33 |
+ |
atom[2]{ |
34 |
+ |
type = "Pchg-"; |
35 |
+ |
position(0.0, 0.0, -1.0); |
36 |
+ |
} |
37 |
+ |
|
38 |
+ |
|
39 |
+ |
rigidBody[0]{ |
40 |
+ |
|
41 |
+ |
members(0, 1, 2); |
42 |
+ |
} |
43 |
+ |
|
44 |
+ |
|
45 |
+ |
cutoffGroup{ |
46 |
+ |
|
47 |
+ |
members(0, 1, 2); |
48 |
+ |
} |
49 |
+ |
} |
50 |
+ |
|
51 |
+ |
molecule{ |
52 |
+ |
name = "PDIP"; |
53 |
+ |
|
54 |
+ |
atom[0]{ |
55 |
+ |
type = "PDIP"; |
56 |
+ |
position( 0.0, 0.0, 0.0 ); |
57 |
+ |
orientation( 0.0, 0.0, 0.0 ); |
58 |
+ |
} |
59 |
+ |
} |
60 |
+ |
|
61 |
+ |
molecule{ |
62 |
|
name = "SSD_E"; |
63 |
< |
nAtoms = 1; |
63 |
> |
|
64 |
|
atom[0]{ |
65 |
|
type = "SSD_E"; |
66 |
|
position( 0.0, 0.0, 0.0 ); |
70 |
|
|
71 |
|
molecule{ |
72 |
|
name = "SSD_RF"; |
73 |
< |
nAtoms = 1; |
73 |
> |
|
74 |
|
atom[0]{ |
75 |
|
type = "SSD_RF"; |
76 |
|
position( 0.0, 0.0, 0.0 ); |
80 |
|
|
81 |
|
molecule{ |
82 |
|
name = "SSD"; |
83 |
< |
nAtoms = 1; |
83 |
> |
|
84 |
|
atom[0]{ |
85 |
|
type = "SSD"; |
86 |
|
position( 0.0, 0.0, 0.0 ); |
90 |
|
|
91 |
|
molecule{ |
92 |
|
name = "SSD1"; |
93 |
< |
nAtoms = 1; |
93 |
> |
|
94 |
|
atom[0]{ |
95 |
|
type = "SSD1"; |
96 |
|
position( 0.0, 0.0, 0.0 ); |
100 |
|
|
101 |
|
molecule{ |
102 |
|
name = "TIP3P"; |
103 |
< |
nAtoms = 3; |
103 |
> |
|
104 |
|
atom[0]{ |
105 |
|
type = "O_TIP3P"; |
106 |
|
position( 0.0, 0.0, -0.06556 ); |
114 |
|
position( 0.0, -0.75695, 0.52032 ); |
115 |
|
} |
116 |
|
|
117 |
< |
nRigidBodies = 1; |
117 |
> |
|
118 |
|
rigidBody[0]{ |
119 |
< |
nMembers = 3; |
119 |
> |
|
120 |
|
members(0, 1, 2); |
121 |
|
} |
122 |
|
|
123 |
< |
nCutoffGroups = 1; |
124 |
< |
cutoffGroup[0]{ |
125 |
< |
nMembers = 3; |
123 |
> |
|
124 |
> |
cutoffGroup{ |
125 |
> |
|
126 |
|
members(0, 1, 2); |
127 |
|
} |
128 |
|
} |
129 |
|
|
130 |
|
molecule{ |
131 |
|
name = "TIP4P"; |
132 |
< |
nAtoms = 4; |
132 |
> |
|
133 |
|
atom[0]{ |
134 |
|
type = "O_TIP4P"; |
135 |
|
position( 0.0, 0.0, -0.06556 ); |
146 |
|
type = "EP_TIP4P"; |
147 |
|
position( 0.0, 0.0, 0.08444 ); |
148 |
|
} |
149 |
< |
nRigidBodies = 1; |
149 |
> |
|
150 |
|
rigidBody[0]{ |
151 |
< |
nMembers = 4; |
151 |
> |
|
152 |
|
members(0, 1, 2, 3); |
153 |
|
} |
154 |
|
|
155 |
< |
nCutoffGroups = 1; |
156 |
< |
cutoffGroup[0]{ |
157 |
< |
nMembers = 4; |
155 |
> |
|
156 |
> |
cutoffGroup{ |
157 |
> |
|
158 |
|
members(0, 1, 2, 3); |
159 |
|
} |
160 |
|
} |
161 |
|
|
162 |
|
molecule{ |
163 |
|
name = "TIP4P-Ew"; |
164 |
< |
nAtoms = 4; |
164 |
> |
|
165 |
|
atom[0]{ |
166 |
|
type = "O_TIP4P-Ew"; |
167 |
|
position( 0.0, 0.0, -0.06556 ); |
178 |
|
type = "EP_TIP4P-Ew"; |
179 |
|
position( 0.0, 0.0, 0.05944 ); |
180 |
|
} |
181 |
< |
nRigidBodies = 1; |
181 |
> |
|
182 |
|
rigidBody[0]{ |
183 |
< |
nMembers = 4; |
183 |
> |
|
184 |
|
members(0, 1, 2, 3); |
185 |
|
} |
186 |
|
|
187 |
< |
nCutoffGroups = 1; |
188 |
< |
cutoffGroup[0]{ |
189 |
< |
nMembers = 4; |
187 |
> |
|
188 |
> |
cutoffGroup{ |
189 |
> |
|
190 |
|
members(0, 1, 2, 3); |
191 |
|
} |
192 |
|
} |
193 |
|
|
194 |
|
molecule{ |
195 |
|
name = "TIP5P"; |
196 |
< |
nAtoms = 5; |
196 |
> |
|
197 |
|
atom[0]{ |
198 |
|
type = "O_TIP5P"; |
199 |
|
position( 0.0, 0.0, -0.06556 ); |
214 |
|
type = "EP_TIP5P"; |
215 |
|
position( -0.57154, 0.0, -0.46971 ); |
216 |
|
} |
217 |
< |
nRigidBodies = 1; |
217 |
> |
|
218 |
|
rigidBody[0]{ |
219 |
< |
nMembers = 5; |
219 |
> |
|
220 |
|
members(0, 1, 2, 3, 4); |
221 |
|
} |
222 |
|
|
223 |
< |
nCutoffGroups = 1; |
224 |
< |
cutoffGroup[0]{ |
225 |
< |
nMembers = 5; |
223 |
> |
|
224 |
> |
cutoffGroup{ |
225 |
> |
|
226 |
|
members(0, 1, 2, 3, 4); |
227 |
|
} |
228 |
|
} |
229 |
|
|
230 |
|
molecule{ |
231 |
|
name = "SPCE"; |
232 |
< |
nAtoms = 3; |
232 |
> |
|
233 |
|
atom[0]{ |
234 |
|
type = "O_SPCE"; |
235 |
|
position( 0.0, 0.0, -0.06461 ); |
242 |
|
type = "H_SPCE"; |
243 |
|
position( 0.0, -0.81649, 0.51275 ); |
244 |
|
} |
245 |
< |
nRigidBodies = 1; |
245 |
> |
|
246 |
|
rigidBody[0]{ |
247 |
< |
nMembers = 3; |
247 |
> |
|
248 |
|
members(0, 1, 2); |
249 |
|
} |
250 |
|
|
251 |
< |
nCutoffGroups = 1; |
252 |
< |
cutoffGroup[0]{ |
253 |
< |
nMembers = 3; |
251 |
> |
|
252 |
> |
cutoffGroup{ |
253 |
> |
|
254 |
|
members(0, 1, 2); |
255 |
|
} |
256 |
|
} |
257 |
|
|
258 |
|
molecule{ |
259 |
|
name = "SPC"; |
260 |
< |
nAtoms = 3; |
260 |
> |
|
261 |
|
atom[0]{ |
262 |
|
type = "O_SPC"; |
263 |
|
position( 0.0, 0.0, -0.06461 ); |
270 |
|
type = "H_SPC"; |
271 |
|
position( 0.0, -0.81649, 0.51275 ); |
272 |
|
} |
273 |
< |
nRigidBodies = 1; |
273 |
> |
|
274 |
|
rigidBody[0]{ |
275 |
< |
nMembers = 3; |
275 |
> |
|
276 |
|
members(0, 1, 2); |
277 |
|
} |
278 |
|
|
279 |
< |
nCutoffGroups = 1; |
280 |
< |
cutoffGroup[0]{ |
281 |
< |
nMembers = 3; |
279 |
> |
|
280 |
> |
cutoffGroup{ |
281 |
> |
|
282 |
|
members(0, 1, 2); |
283 |
|
} |
284 |
|
} |
285 |
|
|
286 |
|
molecule{ |
287 |
|
name = "DPD"; |
288 |
< |
nAtoms = 1; |
288 |
> |
|
289 |
|
atom[0]{ |
290 |
|
type = "DPD"; |
291 |
|
position(0.0, 0.0, 0.0); |