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 |
< |
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{ |
45 |
– |
name = "SHED"; |
46 |
– |
nAtoms = 1; |
47 |
– |
atom[0]{ |
48 |
– |
type = "SHED"; |
49 |
– |
position( 0.0, 0.0, 0.0 ); |
50 |
– |
orientation( 0.0, 0.0, 0.0 ); |
51 |
– |
} |
52 |
– |
} |
53 |
– |
|
54 |
– |
molecule{ |
63 |
|
name = "TIP3P"; |
64 |
< |
nAtoms = 3; |
64 |
> |
|
65 |
|
atom[0]{ |
66 |
|
type = "O_TIP3P"; |
67 |
|
position( 0.0, 0.0, -0.06556 ); |
75 |
|
position( 0.0, -0.75695, 0.52032 ); |
76 |
|
} |
77 |
|
|
78 |
< |
nRigidBodies = 1; |
78 |
> |
|
79 |
|
rigidBody[0]{ |
80 |
< |
nMembers = 3; |
80 |
> |
|
81 |
|
members(0, 1, 2); |
82 |
|
} |
83 |
|
|
84 |
< |
nCutoffGroups = 1; |
85 |
< |
cutoffGroup[0]{ |
86 |
< |
nMembers = 3; |
84 |
> |
|
85 |
> |
cutoffGroup{ |
86 |
> |
|
87 |
|
members(0, 1, 2); |
88 |
|
} |
89 |
|
} |
90 |
|
|
91 |
|
molecule{ |
92 |
|
name = "TIP4P"; |
93 |
< |
nAtoms = 4; |
93 |
> |
|
94 |
|
atom[0]{ |
95 |
|
type = "O_TIP4P"; |
96 |
|
position( 0.0, 0.0, -0.06556 ); |
107 |
|
type = "EP_TIP4P"; |
108 |
|
position( 0.0, 0.0, 0.08444 ); |
109 |
|
} |
110 |
< |
nRigidBodies = 1; |
110 |
> |
|
111 |
|
rigidBody[0]{ |
112 |
< |
nMembers = 4; |
112 |
> |
|
113 |
|
members(0, 1, 2, 3); |
114 |
|
} |
115 |
|
|
116 |
< |
nCutoffGroups = 1; |
117 |
< |
cutoffGroup[0]{ |
118 |
< |
nMembers = 4; |
116 |
> |
|
117 |
> |
cutoffGroup{ |
118 |
> |
|
119 |
|
members(0, 1, 2, 3); |
120 |
|
} |
121 |
|
} |
122 |
|
|
123 |
|
molecule{ |
124 |
|
name = "TIP4P-Ew"; |
125 |
< |
nAtoms = 4; |
125 |
> |
|
126 |
|
atom[0]{ |
127 |
|
type = "O_TIP4P-Ew"; |
128 |
|
position( 0.0, 0.0, -0.06556 ); |
139 |
|
type = "EP_TIP4P-Ew"; |
140 |
|
position( 0.0, 0.0, 0.05944 ); |
141 |
|
} |
142 |
< |
nRigidBodies = 1; |
142 |
> |
|
143 |
|
rigidBody[0]{ |
144 |
< |
nMembers = 4; |
144 |
> |
|
145 |
|
members(0, 1, 2, 3); |
146 |
|
} |
147 |
|
|
148 |
< |
nCutoffGroups = 1; |
149 |
< |
cutoffGroup[0]{ |
150 |
< |
nMembers = 4; |
148 |
> |
|
149 |
> |
cutoffGroup{ |
150 |
> |
|
151 |
|
members(0, 1, 2, 3); |
152 |
|
} |
153 |
|
} |
154 |
|
|
155 |
|
molecule{ |
156 |
|
name = "TIP5P"; |
157 |
< |
nAtoms = 5; |
157 |
> |
|
158 |
|
atom[0]{ |
159 |
|
type = "O_TIP5P"; |
160 |
|
position( 0.0, 0.0, -0.06556 ); |
175 |
|
type = "EP_TIP5P"; |
176 |
|
position( -0.57154, 0.0, -0.46971 ); |
177 |
|
} |
178 |
< |
nRigidBodies = 1; |
178 |
> |
|
179 |
|
rigidBody[0]{ |
180 |
< |
nMembers = 5; |
180 |
> |
|
181 |
|
members(0, 1, 2, 3, 4); |
182 |
|
} |
183 |
|
|
184 |
< |
nCutoffGroups = 1; |
185 |
< |
cutoffGroup[0]{ |
186 |
< |
nMembers = 5; |
184 |
> |
|
185 |
> |
cutoffGroup{ |
186 |
> |
|
187 |
|
members(0, 1, 2, 3, 4); |
188 |
|
} |
189 |
|
} |
190 |
|
|
191 |
|
molecule{ |
192 |
|
name = "SPCE"; |
193 |
< |
nAtoms = 3; |
193 |
> |
|
194 |
|
atom[0]{ |
195 |
|
type = "O_SPCE"; |
196 |
|
position( 0.0, 0.0, -0.06461 ); |
203 |
|
type = "H_SPCE"; |
204 |
|
position( 0.0, -0.81649, 0.51275 ); |
205 |
|
} |
206 |
< |
nRigidBodies = 1; |
206 |
> |
|
207 |
|
rigidBody[0]{ |
208 |
< |
nMembers = 3; |
208 |
> |
|
209 |
|
members(0, 1, 2); |
210 |
|
} |
211 |
|
|
212 |
< |
nCutoffGroups = 1; |
213 |
< |
cutoffGroup[0]{ |
214 |
< |
nMembers = 3; |
212 |
> |
|
213 |
> |
cutoffGroup{ |
214 |
> |
|
215 |
|
members(0, 1, 2); |
216 |
|
} |
217 |
|
} |
218 |
|
|
219 |
|
molecule{ |
220 |
|
name = "SPC"; |
221 |
< |
nAtoms = 3; |
221 |
> |
|
222 |
|
atom[0]{ |
223 |
|
type = "O_SPC"; |
224 |
|
position( 0.0, 0.0, -0.06461 ); |
231 |
|
type = "H_SPC"; |
232 |
|
position( 0.0, -0.81649, 0.51275 ); |
233 |
|
} |
234 |
< |
nRigidBodies = 1; |
234 |
> |
|
235 |
|
rigidBody[0]{ |
236 |
< |
nMembers = 3; |
236 |
> |
|
237 |
|
members(0, 1, 2); |
238 |
|
} |
239 |
|
|
240 |
< |
nCutoffGroups = 1; |
241 |
< |
cutoffGroup[0]{ |
242 |
< |
nMembers = 3; |
240 |
> |
|
241 |
> |
cutoffGroup{ |
242 |
> |
|
243 |
|
members(0, 1, 2); |
244 |
|
} |
245 |
|
} |
246 |
|
|
247 |
|
molecule{ |
248 |
|
name = "DPD"; |
249 |
< |
nAtoms = 1; |
249 |
> |
|
250 |
|
atom[0]{ |
251 |
|
type = "DPD"; |
252 |
|
position(0.0, 0.0, 0.0); |