- Posts: 13
simulation blow up in the protein in water simulation
- junfeng
- Topic Author
- Offline
- Fresh Boarder
Less
More
11 years 3 months ago - 11 years 3 months ago #1355
by junfeng
simulation blow up in the protein in water simulation was created by junfeng
I am following the protein in water tutorial. After I solvated ubiquitin in water, I carried out minimization and position restraint simulation with the given em.mdp and md.mdp file. But during minimization, the water went scattered (I can see some empty space using vmd). position restraint simulation crash because of failure of LINCS constraint which indicates the system blows up.
The solvated ubiquitin in water looks fine. But the minimized pdb has empty spaces in water. There must be some errors but I could not figure out what went wrong.
Additional Qs:
How to use stiff bond for minimization? I do not know what it corresponds to in mdp file.
Do I need to add ions to the system to make it neutral for martini simulation?
The solvated ubiquitin in water looks fine. But the minimized pdb has empty spaces in water. There must be some errors but I could not figure out what went wrong.
Additional Qs:
How to use stiff bond for minimization? I do not know what it corresponds to in mdp file.
Do I need to add ions to the system to make it neutral for martini simulation?
Please Log in or Create an account to join the conversation.
- djurre
- Offline
- Admin
Less
More
- Posts: 272
11 years 3 months ago #1359
by djurre
Replied by djurre on topic simulation blow up in the protein in water simulation
Scattering water: Hard to say what is happening, but could it be the the order of molecules in the top and gro/pdb file is different? And does the water in the solvated structure look normal, eg no areas where the density of the water is higher then else where?
Stiff bonds for minimization: Do you mean replacing constraints by stiff bonds during minimization? In my experience that is not really needed in most situations.
Adding ions: Neutralizing your systems doesn't hurt.
Stiff bonds for minimization: Do you mean replacing constraints by stiff bonds during minimization? In my experience that is not really needed in most situations.
Adding ions: Neutralizing your systems doesn't hurt.
Please Log in or Create an account to join the conversation.
- junfeng
- Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 13
11 years 3 months ago #1363
by junfeng
Replied by junfeng on topic simulation blow up in the protein in water simulation
I checked the gro file, protein first then water.
In the top file:
#include "martini_v2.1.itp"
#include "Protein_A.itp"
[ system ]
; name
Martini system from 1UBQ.pdb
[ molecules ]
; name number
Protein_A 1
W 890
As I said the solvated structure looks normal, Ubiquitin is at the center of box surrounded by W. the water density looks even everywhere. I pasted the gro file so maybe people can find sth wrong there.
I am able to run protein alone in vacumm without error for 500000 steps. I am able to run water box alone without error for 116100 steps. But when I run protein in water, something went wrong within a few thousand steps.
I noted in mdp file of protein simulation, I cannot put Protein_A as energygrps. I got error messages when "grompp". Why?
How can I add ions to solvated box? Can you give me an example of gromacs command?
Here is the gro file of protein in water:
Martini system from 1UBQ.pdb
1053
1MET BB 1 2.152 2.287 1.804
1MET SC1 2 1.987 2.050 2.057
2GLN BB 3 2.121 2.519 1.953
2GLN SC1 4 2.197 2.804 1.709
3ILE BB 5 2.202 2.616 2.253
3ILE SC1 6 2.142 2.371 2.433
4PHE BB 7 2.185 2.911 2.449
4PHE SC1 8 2.053 3.077 2.241
4PHE SC2 9 2.124 3.227 2.027
4PHE SC3 10 1.894 3.086 2.023
5VAL BB 11 2.334 3.056 2.718
5VAL SC1 12 2.489 2.863 2.815
6LYS BB 13 2.299 3.324 2.927
6LYS SC1 14 2.062 3.515 2.910
6LYS SC2 15 1.866 3.685 2.922
7THR BB 16 2.508 3.487 3.156
7THR SC1 17 2.755 3.454 3.084
8LEU BB 18 2.395 3.747 3.326
8LEU SC1 19 2.413 3.638 3.633
9THR BB 20 2.598 4.000 3.158
9THR SC1 21 2.852 3.943 3.157
10GLY BB 22 2.416 3.921 2.850
11LYS BB 23 2.552 3.743 2.720
11LYS SC1 24 2.872 3.737 2.672
11LYS SC2 25 2.983 3.655 2.434
12THR BB 26 2.474 3.484 2.480
12THR SC1 27 2.217 3.500 2.442
13ILE BB 28 2.646 3.219 2.350
13ILE SC1 29 2.844 3.114 2.565
14THR BB 30 2.559 2.957 2.115
14THR SC1 31 2.592 3.061 1.879
15LEU BB 32 2.681 2.614 2.112
15LEU SC1 33 2.713 2.588 2.435
16GLU BB 34 2.645 2.338 1.958
16GLU SC1 35 2.592 2.472 1.598
17VAL BB 36 2.494 2.033 2.113
17VAL SC1 37 2.551 2.095 2.364
18GLU BB 38 2.336 1.734 2.108
18GLU SC1 39 2.386 1.580 1.765
19PRO BB 40 2.108 1.629 2.321
19PRO SC1 41 1.855 1.567 2.177
20SER BB 42 2.336 1.352 2.431
20SER SC1 43 2.403 1.231 2.219
21ASP BB 44 2.553 1.580 2.566
21ASP SC1 45 2.767 1.623 2.347
22THR BB 46 2.659 1.545 2.857
22THR SC1 47 2.816 1.344 2.904
23ILE BB 48 2.728 1.795 3.142
23ILE SC1 49 2.442 1.915 3.153
24GLU BB 50 3.022 1.778 3.101
24GLU SC1 51 3.165 1.462 3.267
25ASN BB 52 3.008 1.880 2.758
25ASN SC1 53 3.194 1.693 2.611
26VAL BB 54 2.881 2.170 2.814
26VAL SC1 55 2.627 2.243 2.825
27LYS BB 56 3.126 2.267 3.027
27LYS SC1 57 2.967 2.211 3.313
27LYS SC2 58 2.783 2.222 3.513
28ALA BB 59 3.382 2.220 2.800
29LYS BB 60 3.250 2.425 2.551
29LYS SC1 61 3.075 2.236 2.370
29LYS SC2 62 3.013 2.034 2.206
30ILE BB 63 3.243 2.684 2.749
30ILE SC1 64 2.952 2.707 2.855
31GLN BB 65 3.560 2.701 2.817
31GLN SC1 66 3.791 2.493 3.044
32ASP BB 67 3.675 2.724 2.500
32ASP SC1 68 3.727 2.434 2.395
33LYS BB 69 3.504 3.009 2.436
33LYS SC1 70 3.230 2.894 2.296
33LYS SC2 71 3.069 2.953 2.091
34GLU BB 72 3.625 3.197 2.700
34GLU SC1 73 3.252 3.339 2.727
35GLY BB 74 3.723 3.099 3.039
36ILE BB 75 3.485 2.948 3.242
36ILE SC1 76 3.235 3.117 3.172
37PRO BB 77 3.555 2.721 3.420
37PRO SC1 78 3.828 2.762 3.540
38PRO BB 79 3.438 2.418 3.543
38PRO SC1 80 3.502 2.209 3.344
39ASP BB 81 3.325 2.472 3.812
39ASP SC1 82 3.530 2.512 4.056
40GLN BB 83 3.163 2.756 3.793
40GLN SC1 84 3.480 2.980 3.848
41GLN BB 85 2.937 2.747 3.670
41GLN SC1 86 3.064 2.672 3.314
42ARG BB 87 2.624 2.654 3.713
42ARG SC1 88 2.531 2.743 4.000
42ARG SC2 89 2.248 2.813 4.159
43LEU BB 90 2.359 2.566 3.516
43LEU SC1 91 2.522 2.526 3.231
44ILE BB 92 2.002 2.618 3.516
44ILE SC1 93 1.972 2.819 3.750
45PHE BB 94 1.743 2.570 3.342
45PHE SC1 95 1.640 2.429 3.103
45PHE SC2 96 1.467 2.224 3.068
45PHE SC3 97 1.413 2.466 2.960
46ALA BB 98 1.396 2.573 3.501
47GLY BB 99 1.515 2.604 3.793
48LYS BB 100 1.723 2.291 3.791
48LYS SC1 101 1.471 2.107 3.720
48LYS SC2 102 1.334 2.030 3.500
49GLN BB 103 2.028 2.173 3.789
49GLN SC1 104 2.283 2.307 4.051
50LEU BB 105 2.244 2.084 3.578
50LEU SC1 106 2.084 2.197 3.305
51GLU BB 107 2.444 1.810 3.630
51GLU SC1 108 2.329 1.547 3.903
52ASP BB 109 2.743 1.594 3.595
52ASP SC1 110 2.983 1.790 3.636
53GLY BB 111 2.663 1.364 3.386
54ARG BB 112 2.378 1.448 3.283
54ARG SC1 113 2.181 1.313 3.489
54ARG SC2 114 2.226 1.007 3.567
55THR BB 115 2.206 1.433 2.962
55THR SC1 116 2.252 1.188 2.887
56LEU BB 117 2.064 1.667 2.829
56LEU SC1 118 2.255 1.903 2.705
57SER BB 119 1.782 1.450 2.694
57SER SC1 120 1.857 1.248 2.576
58ASP BB 121 1.644 1.431 3.001
58ASP SC1 122 1.808 1.215 3.168
59TYR BB 123 1.547 1.744 3.042
59TYR SC1 124 1.740 1.833 3.257
59TYR SC2 125 1.801 1.800 3.518
59TYR SC3 126 1.979 1.729 3.328
60ASN BB 127 1.447 1.837 2.731
60ASN SC1 128 1.169 1.718 2.690
61ILE BB 129 1.691 1.949 2.562
61ILE SC1 130 1.840 2.113 2.779
62GLN BB 131 1.551 2.064 2.277
62GLN SC1 132 1.179 1.974 2.233
63LYS BB 133 1.607 2.348 2.062
63LYS SC1 134 1.576 2.217 1.774
63LYS SC2 135 1.381 2.270 1.590
64GLU BB 136 1.646 2.659 2.083
64GLU SC1 137 1.684 2.704 1.693
65SER BB 138 1.731 2.688 2.438
65SER SC1 139 1.655 2.481 2.542
66THR BB 140 1.797 2.883 2.786
66THR SC1 141 1.805 3.134 2.718
67LEU BB 142 2.047 2.773 3.004
67LEU SC1 143 2.142 2.487 2.909
68HIS BB 144 2.226 2.960 3.239
68HIS SC1 145 1.974 3.118 3.324
68HIS SC2 146 1.714 3.070 3.273
68HIS SC3 147 1.802 3.324 3.295
69LEU BB 148 2.482 3.055 3.415
69LEU SC1 149 2.736 2.997 3.234
70VAL BB 150 2.582 3.160 3.723
70VAL SC1 151 2.360 3.194 3.863
71LEU BB 152 2.884 3.175 3.914
71LEU SC1 153 3.083 3.238 3.658
72ARG BB 154 3.068 3.054 4.190
72ARG SC1 155 2.995 2.749 4.256
72ARG SC2 156 2.923 2.450 4.126
73LEU BB 157 3.329 3.153 4.300
73LEU SC1 158 3.412 3.409 4.107
74ARG BB 159 3.571 3.093 4.473
74ARG SC1 160 3.635 2.778 4.489
74ARG SC2 161 3.899 2.590 4.408
75GLY BB 162 3.664 3.309 4.689
76GLY BB 163 3.500 3.545 4.915
77W W 164 3.047 1.499 1.968
78W W 165 1.142 1.573 1.846
79W W 166 2.768 1.197 5.465
80W W 167 3.487 4.695 0.764
81W W 168 0.340 3.819 1.422
82W W 169 1.460 3.839 0.236
83W W 170 0.944 3.320 0.294
84W W 171 3.694 2.328 1.393
85W W 172 3.051 1.355 1.461
86W W 173 0.634 2.079 1.950
87W W 174 0.857 2.175 3.210
88W W 175 2.651 3.496 1.875
89W W 176 3.719 1.104 1.895
90W W 177 2.236 2.217 1.157
91W W 178 1.595 1.440 1.735
92W W 179 2.991 0.117 2.646
93W W 180 2.937 4.745 5.543
94W W 181 3.450 1.639 1.566
95W W 182 3.496 3.677 2.117
96W W 183 0.286 1.101 5.328
97W W 184 1.680 1.470 1.502
98W W 185 3.453 0.918 0.840
99W W 186 3.546 1.811 4.681
100W W 187 1.276 1.352 0.456
101W W 188 2.381 1.221 0.220
102W W 189 2.864 3.087 1.557
103W W 190 1.308 1.555 1.948
104W W 191 3.434 4.738 3.825
105W W 192 4.369 3.940 1.819
106W W 193 4.513 3.616 4.145
107W W 194 3.509 1.804 5.844
108W W 195 2.360 3.121 4.554
109W W 196 2.395 1.724 0.099
110W W 197 1.908 1.940 1.431
111W W 198 3.258 2.675 4.525
112W W 199 3.876 3.335 5.588
113W W 200 4.765 3.189 4.006
114W W 201 1.584 2.062 0.209
115W W 202 3.546 2.657 1.907
116W W 203 3.028 2.266 4.785
117W W 204 3.623 0.215 5.678
118W W 205 4.795 4.106 5.470
119W W 206 3.841 2.685 5.863
120W W 207 4.675 0.240 4.873
121W W 208 2.099 2.856 5.824
122W W 209 1.976 3.571 4.398
123W W 210 1.578 0.061 5.746
124W W 211 1.612 4.299 5.498
125W W 212 2.731 2.336 5.178
126W W 213 0.200 2.837 1.474
127W W 214 3.218 2.346 5.279
128W W 215 1.592 2.115 4.217
129W W 216 1.286 2.043 5.771
130W W 217 0.695 3.916 1.139
131W W 218 2.308 1.262 5.695
132W W 219 4.155 1.174 0.963
133W W 220 3.468 2.801 5.120
134W W 221 1.715 2.034 4.730
135W W 222 1.318 3.688 2.418
136W W 223 4.483 0.750 5.123
137W W 224 2.230 0.074 3.649
138W W 225 2.867 1.290 4.196
139W W 226 1.447 3.942 5.202
140W W 227 2.599 2.079 4.661
141W W 228 0.833 0.014 1.345
142W W 229 3.486 1.777 5.308
143W W 230 1.864 0.415 1.765
144W W 231 0.180 3.064 1.933
145W W 232 4.782 4.181 0.994
146W W 233 1.757 0.469 0.721
147W W 234 1.490 3.104 5.105
148W W 235 3.669 3.508 1.601
149W W 236 3.707 3.601 0.552
150W W 237 4.382 3.363 2.191
151W W 238 0.798 1.757 1.151
152W W 239 1.057 2.253 5.449
153W W 240 0.871 1.352 4.218
154W W 241 3.788 1.336 3.231
155W W 242 1.306 1.823 4.580
156W W 243 0.877 1.045 0.597
157W W 244 0.002 4.174 0.586
158W W 245 2.964 1.873 1.414
159W W 246 3.341 1.243 4.529
160W W 247 3.188 3.108 4.813
161W W 248 0.148 0.584 5.437
162W W 249 2.617 2.135 4.517
163W W 250 1.034 3.332 2.009
164W W 251 0.587 4.881 2.614
165W W 252 3.141 2.762 1.534
166W W 253 1.082 3.905 3.825
167W W 254 1.600 4.450 4.430
168W W 255 1.578 3.581 1.980
169W W 256 4.747 2.785 1.199
170W W 257 2.677 4.903 3.617
171W W 258 0.005 1.514 3.551
172W W 259 3.300 3.529 4.511
173W W 260 0.979 3.827 2.859
174W W 261 3.719 4.029 1.836
175W W 262 3.897 0.902 3.391
176W W 263 2.320 2.933 1.295
177W W 264 3.029 0.843 0.562
178W W 265 0.526 4.110 2.787
179W W 266 3.316 3.267 1.298
180W W 267 1.343 3.129 2.346
181W W 268 2.122 0.167 1.482
182W W 269 1.506 3.387 4.633
183W W 270 3.830 4.765 2.910
184W W 271 1.326 1.535 5.474
185W W 272 1.016 3.874 5.661
186W W 273 1.859 3.416 4.968
187W W 274 3.699 1.744 3.351
188W W 275 2.947 4.349 4.857
189W W 276 1.563 3.055 1.339
190W W 277 4.438 3.327 0.252
191W W 278 1.649 2.949 5.896
192W W 279 2.639 2.054 4.016
193W W 280 3.471 1.634 4.235
194W W 281 2.784 3.641 3.881
195W W 282 1.407 0.980 5.563
196W W 283 3.072 3.870 3.531
197W W 284 0.887 1.734 4.937
198W W 285 1.377 4.508 3.550
199W W 286 1.559 0.628 0.063
200W W 287 3.081 2.504 2.025
201W W 288 2.164 4.168 5.469
202W W 289 2.143 1.187 1.592
203W W 290 3.239 2.268 1.021
204W W 291 1.651 1.555 4.343
205W W 292 3.511 4.329 4.769
206W W 293 1.532 0.046 3.660
207W W 294 3.967 0.910 1.579
208W W 295 3.064 1.646 1.941
209W W 296 3.647 1.157 5.918
210W W 297 1.082 1.659 0.749
211W W 298 4.541 0.430 5.574
212W W 299 3.289 4.796 1.282
213W W 300 1.539 1.429 2.333
214W W 301 4.384 1.896 4.890
215W W 302 4.230 2.996 5.789
216W W 303 3.325 4.443 4.266
217W W 304 2.093 3.351 0.972
218W W 305 1.262 0.745 3.491
219W W 306 1.069 2.129 3.835
220W W 307 1.321 0.415 1.064
221W W 308 1.888 1.099 1.099
222W W 309 3.580 1.142 2.489
223W W 310 4.540 0.290 1.581
224W W 311 2.798 0.721 5.678
225W W 312 0.571 4.609 1.746
226W W 313 0.857 4.613 1.006
227W W 314 2.088 2.351 4.765
228W W 315 3.495 1.424 0.854
229W W 316 4.754 2.360 4.732
230W W 317 0.942 3.814 0.256
231W W 318 0.203 1.876 4.781
232W W 319 0.723 0.871 5.765
233W W 320 0.508 4.591 5.121
234W W 321 0.277 4.294 0.982
235W W 322 3.729 2.151 1.859
236W W 323 3.377 2.197 0.534
237W W 324 0.785 2.280 5.879
238W W 325 2.151 1.789 4.668
239W W 326 4.616 0.073 2.582
240W W 327 3.731 3.568 3.629
241W W 328 1.729 0.470 4.201
242W W 329 1.444 1.369 3.637
243W W 330 1.863 2.815 5.428
244W W 331 2.550 4.564 4.414
245W W 332 4.412 2.541 5.223
246W W 333 4.168 1.913 3.522
247W W 334 3.509 4.742 5.008
248W W 335 1.788 3.571 1.492
249W W 336 0.045 2.778 2.877
250W W 337 4.845 3.134 2.773
251W W 338 2.943 1.005 4.751
252W W 339 1.260 0.622 1.557
253W W 340 4.803 2.569 0.716
254W W 341 0.130 4.530 4.378
255W W 342 3.123 1.464 5.701
256W W 343 3.420 1.869 2.032
257W W 344 3.431 1.374 2.226
258W W 345 3.451 1.797 2.313
259W W 346 1.998 0.340 5.875
260W W 347 2.906 0.661 5.206
261W W 348 2.200 1.342 4.206
262W W 349 0.633 0.269 5.091
263W W 350 1.370 3.425 0.231
264W W 351 0.021 2.985 3.662
265W W 352 3.262 0.342 0.060
266W W 353 4.701 2.998 5.275
267W W 354 0.484 2.863 1.156
268W W 355 1.462 3.045 1.976
269W W 356 3.008 0.964 1.178
270W W 357 4.339 0.881 0.529
271W W 358 0.060 3.849 3.387
272W W 359 1.825 3.803 1.087
273W W 360 4.705 2.050 0.163
274W W 361 3.685 3.466 3.443
275W W 362 0.159 3.876 5.295
276W W 363 2.479 1.114 1.226
277W W 364 1.806 3.727 3.931
278W W 365 4.297 1.625 1.091
279W W 366 3.283 2.231 1.618
280W W 367 3.620 1.563 3.688
281W W 368 1.455 3.399 5.765
282W W 369 3.927 3.201 3.808
283W W 370 3.638 4.496 2.127
284W W 371 0.893 2.509 4.000
285W W 372 3.914 1.824 5.559
286W W 373 4.642 1.119 1.820
287W W 374 1.285 2.649 5.235
288W W 375 1.903 3.340 5.476
289W W 376 0.793 4.308 5.788
290W W 377 2.521 1.346 4.665
291W W 378 4.306 4.777 2.876
292W W 379 4.386 1.685 5.423
293W W 380 3.514 1.810 0.657
294W W 381 0.098 2.141 5.973
295W W 382 3.115 4.560 2.263
296W W 383 3.433 0.880 4.875
297W W 384 3.018 0.584 1.899
298W W 385 3.090 0.018 3.758
299W W 386 2.236 3.768 0.939
300W W 387 1.317 3.000 3.724
301W W 388 3.089 1.772 0.640
302W W 389 3.643 4.860 3.385
303W W 390 4.387 4.409 5.415
304W W 391 0.930 0.201 2.243
305W W 392 1.446 1.532 0.921
306W W 393 1.921 0.929 2.313
307W W 394 1.448 4.867 5.395
308W W 395 4.398 4.776 2.226
309W W 396 4.284 2.367 4.149
310W W 397 4.265 3.387 5.254
311W W 398 4.945 0.711 4.719
312W W 399 1.831 4.615 5.784
313W W 400 0.381 1.156 0.442
314W W 401 2.409 0.818 5.969
315W W 402 3.958 0.398 4.333
316W W 403 1.220 2.586 2.536
317W W 404 3.981 1.153 0.355
318W W 405 3.175 3.106 5.429
319W W 406 4.861 2.907 2.262
320W W 407 0.534 3.494 0.030
321W W 408 3.001 1.692 4.527
322W W 409 1.617 1.070 3.536
323W W 410 0.021 4.689 0.409
324W W 411 4.825 1.340 3.129
325W W 412 1.386 0.702 2.804
326W W 413 2.856 3.754 0.384
327W W 414 1.759 1.409 0.641
328W W 415 1.914 2.408 5.737
329W W 416 0.701 3.322 3.003
330W W 417 4.684 0.251 3.169
331W W 418 4.437 4.376 3.183
332W W 419 4.891 4.490 5.329
333W W 420 1.186 4.695 5.874
334W W 421 2.831 3.191 1.517
335W W 422 4.709 4.700 0.017
336W W 423 1.244 4.753 1.983
337W W 424 3.781 4.387 3.925
338W W 425 4.116 0.047 2.483
339W W 426 3.995 3.644 1.940
340W W 427 2.910 4.225 1.497
341W W 428 3.668 2.942 1.524
342W W 429 4.177 2.123 5.266
343W W 430 2.155 3.395 5.895
344W W 431 4.934 3.653 0.960
345W W 432 3.974 4.648 5.765
346W W 433 4.622 4.361 2.123
347W W 434 2.553 0.107 0.853
348W W 435 1.969 3.343 4.144
349W W 436 1.860 3.067 4.263
350W W 437 4.715 1.394 4.453
351W W 438 3.622 3.821 5.705
352W W 439 4.291 1.642 3.135
353W W 440 2.671 2.592 4.535
354W W 441 4.438 1.310 5.773
355W W 442 0.368 3.385 1.456
356W W 443 4.866 3.627 1.394
357W W 444 2.454 1.041 3.210
358W W 445 4.745 0.661 3.670
359W W 446 2.608 1.830 0.461
360W W 447 3.658 2.272 0.856
361W W 448 3.395 2.182 4.410
362W W 449 0.580 3.221 2.092
363W W 450 1.574 3.869 5.810
364W W 451 3.538 0.490 1.743
365W W 452 0.072 0.829 1.921
366W W 453 4.970 2.906 5.729
367W W 454 3.043 2.732 1.200
368W W 455 4.481 0.164 5.921
369W W 456 2.106 4.600 3.451
370W W 457 3.944 3.032 1.854
371W W 458 1.520 1.903 1.251
372W W 459 1.808 2.689 4.119
373W W 460 0.820 3.653 2.279
374W W 461 4.788 3.505 5.007
375W W 462 4.220 2.799 0.163
376W W 463 4.062 3.500 2.738
377W W 464 3.583 0.236 4.594
378W W 465 0.181 3.367 5.367
379W W 466 3.964 4.823 0.237
380W W 467 0.949 2.615 3.284
381W W 468 1.465 3.561 2.344
382W W 469 3.925 1.861 1.078
383W W 470 4.517 3.873 1.356
384W W 471 1.379 0.003 1.227
385W W 472 3.049 2.336 1.700
386W W 473 4.868 4.659 2.479
387W W 474 2.602 2.406 0.810
388W W 475 0.321 4.828 2.209
389W W 476 1.312 2.727 0.323
390W W 477 2.555 0.554 1.063
391W W 478 4.500 1.215 3.407
392W W 479 1.863 3.848 5.396
393W W 480 3.899 1.558 1.893
394W W 481 0.454 2.108 1.378
395W W 482 2.042 0.821 3.171
396W W 483 3.942 1.749 4.931
397W W 484 4.055 0.580 4.917
398W W 485 1.530 0.491 2.074
399W W 486 2.453 1.282 4.717
400W W 487 0.594 2.861 0.199
401W W 488 3.067 4.312 0.903
402W W 489 1.514 0.130 4.890
403W W 490 1.628 2.649 4.694
404W W 491 0.434 3.845 2.366
405W W 492 1.513 4.659 0.634
406W W 493 2.587 0.696 1.512
407W W 494 3.160 3.405 1.765
408W W 495 4.700 4.049 3.891
409W W 496 2.860 0.214 3.357
410W W 497 0.811 3.212 1.136
411W W 498 2.450 4.171 0.347
412W W 499 0.007 3.621 0.008
413W W 500 1.742 4.622 5.059
414W W 501 2.638 0.119 4.182
415W W 502 3.987 4.647 4.607
416W W 503 0.646 1.345 3.336
417W W 504 4.445 3.917 5.822
418W W 505 2.977 0.974 2.712
419W W 506 1.818 2.797 1.307
420W W 507 0.079 2.037 3.438
421W W 508 4.763 1.237 5.017
422W W 509 0.052 0.129 2.659
423W W 510 3.089 0.502 0.920
424W W 511 2.922 1.155 1.759
425W W 512 2.917 1.838 1.536
426W W 513 2.171 1.568 0.569
427W W 514 1.973 0.832 0.536
428W W 515 1.446 0.049 0.781
429W W 516 2.697 0.978 3.757
430W W 517 2.255 4.212 2.592
431W W 518 1.265 4.100 3.459
432W W 519 3.468 4.968 0.012
433W W 520 4.799 3.523 2.989
434W W 521 1.170 0.234 3.479
435W W 522 0.247 0.562 3.521
436W W 523 0.188 1.109 3.417
437W W 524 3.139 0.094 0.544
438W W 525 4.207 0.219 5.256
439W W 526 3.124 4.375 5.340
440W W 527 3.274 0.221 4.900
441W W 528 1.118 4.889 4.486
442W W 529 1.126 0.599 5.672
443W W 530 0.931 4.800 5.180
444W W 531 2.527 1.764 4.286
445W W 532 0.207 0.029 5.246
446W W 533 3.265 0.913 4.146
447W W 534 4.978 0.884 1.392
448W W 535 3.811 0.754 1.006
449W W 536 4.331 4.872 5.613
450W W 537 1.113 1.766 0.288
451W W 538 0.208 3.887 0.276
452W W 539 4.000 3.952 5.541
453W W 540 0.007 3.432 3.395
454W W 541 3.821 3.655 0.978
455W W 542 1.585 1.715 5.144
456W W 543 0.162 2.704 0.193
457W W 544 0.945 4.969 0.672
458W W 545 2.898 4.990 2.025
459W W 546 4.113 3.078 0.495
460W W 547 2.367 2.855 0.626
461W W 548 0.898 4.727 0.256
462W W 549 1.067 4.590 3.234
463W W 550 0.587 0.371 2.510
464W W 551 2.889 4.558 1.211
465W W 552 1.132 0.657 2.070
466W W 553 1.656 0.678 4.976
467W W 554 1.133 2.238 0.939
468W W 555 2.004 1.861 4.879
469W W 556 4.554 0.184 0.873
470W W 557 0.636 0.669 0.553
471W W 558 4.975 0.845 5.154
472W W 559 0.047 2.549 3.703
473W W 560 0.285 0.029 3.163
474W W 561 4.130 2.206 2.191
475W W 562 2.774 2.311 1.207
476W W 563 2.011 1.339 4.720
477W W 564 4.651 4.275 4.366
478W W 565 4.009 0.794 0.015
479W W 566 1.014 0.447 4.293
480W W 567 4.243 2.546 4.638
481W W 568 2.284 1.151 0.835
482W W 569 2.726 1.203 0.540
483W W 570 0.060 0.678 0.518
484W W 571 2.569 4.511 5.593
485W W 572 1.788 1.123 5.782
486W W 573 4.451 3.811 5.108
487W W 574 2.033 0.156 0.461
488W W 575 1.147 2.426 4.581
489W W 576 2.324 0.893 4.399
490W W 577 3.548 1.855 1.862
491W W 578 0.270 3.998 4.096
492W W 579 0.833 0.491 1.697
493W W 580 0.346 1.670 5.846
494W W 581 0.710 0.338 0.888
495W W 582 3.673 0.525 3.739
496W W 583 3.651 4.156 4.275
497W W 584 0.890 4.477 4.533
498W W 585 2.809 3.842 1.248
499W W 586 1.198 2.096 5.085
500W W 587 2.487 2.226 0.368
501W W 588 3.174 1.970 4.116
502W W 589 0.934 4.247 1.284
503W W 590 0.683 1.581 1.668
504W W 591 0.516 3.343 4.466
505W W 592 4.450 2.455 0.486
506W W 593 0.168 4.393 2.938
507W W 594 0.165 2.598 1.935
508W W 595 3.342 3.937 4.018
509W W 596 0.196 2.268 1.018
510W W 597 4.923 0.158 0.167
511W W 598 4.849 2.243 1.450
512W W 599 4.935 0.068 5.670
513W W 600 1.305 4.114 1.564
514W W 601 3.554 4.522 2.586
515W W 602 1.628 2.326 1.226
516W W 603 3.242 4.137 2.794
517W W 604 2.062 0.466 3.553
518W W 605 1.365 4.726 2.718
519W W 606 4.557 0.896 0.132
520W W 607 2.958 1.439 0.116
521W W 608 4.900 3.236 4.547
522W W 609 1.142 4.556 1.578
523W W 610 3.764 3.278 0.174
524W W 611 2.014 0.624 4.492
525W W 612 4.898 0.424 1.230
526W W 613 4.798 3.828 0.462
527W W 614 0.534 1.816 3.305
528W W 615 4.108 4.621 0.986
529W W 616 0.358 3.435 3.859
530W W 617 0.963 2.697 2.853
531W W 618 0.806 0.467 2.973
532W W 619 0.207 3.322 0.492
533W W 620 4.553 1.840 2.644
534W W 621 4.791 4.415 3.409
535W W 622 1.943 0.818 1.442
536W W 623 1.393 4.079 4.304
537W W 624 4.603 2.883 3.591
538W W 625 1.638 4.787 1.524
539W W 626 2.208 3.501 1.748
540W W 627 0.469 1.130 2.827
541W W 628 4.321 4.645 1.615
542W W 629 1.061 0.814 1.219
543W W 630 0.093 0.170 1.606
544W W 631 3.157 3.574 0.655
545W W 632 4.730 4.761 1.702
546W W 633 1.472 0.957 2.147
547W W 634 4.518 0.501 4.306
548W W 635 3.473 2.434 4.512
549W W 636 0.724 4.020 4.989
550W W 637 0.769 2.493 1.784
551W W 638 4.905 2.492 5.386
552W W 639 1.654 0.604 3.129
553W W 640 3.856 2.828 1.172
554W W 641 3.378 1.097 3.004
555W W 642 4.305 1.857 5.888
556W W 643 3.388 2.594 2.041
557W W 644 2.298 0.488 3.991
558W W 645 1.159 1.678 3.459
559W W 646 1.349 2.367 4.551
560W W 647 2.062 0.484 2.272
561W W 648 1.435 3.056 1.815
562W W 649 3.844 0.033 3.944
563W W 650 0.924 1.158 0.122
564W W 651 3.340 0.246 3.261
565W W 652 0.585 0.858 0.951
566W W 653 0.948 1.918 1.655
567W W 654 1.324 3.436 1.296
568W W 655 2.565 2.755 0.160
569W W 656 0.106 1.283 1.763
570W W 657 1.935 0.903 4.097
571W W 658 0.633 1.493 5.192
572W W 659 0.670 1.788 3.981
573W W 660 0.320 4.769 0.836
574W W 661 0.345 2.075 4.303
575W W 662 1.365 0.326 0.448
576W W 663 1.121 1.378 1.414
577W W 664 2.693 3.581 4.405
578W W 665 2.184 3.005 4.600
579W W 666 4.220 2.424 1.151
580W W 667 0.839 0.815 3.366
581W W 668 4.187 0.588 2.406
582W W 669 1.233 3.061 5.567
583W W 670 3.480 3.282 0.843
584W W 671 2.930 3.308 4.513
585W W 672 4.775 4.737 3.030
586W W 673 0.221 4.318 4.971
587W W 674 3.016 2.995 0.283
588W W 675 1.831 2.142 0.711
589W W 676 4.694 4.150 4.996
590W W 677 4.979 2.856 4.737
591W W 678 4.779 2.045 0.782
592W W 679 1.506 1.969 4.717
593W W 680 2.718 3.753 5.908
594W W 681 1.621 4.101 2.925
595W W 682 1.286 1.724 4.032
596W W 683 4.597 2.109 5.568
597W W 684 0.742 0.726 4.492
598W W 685 0.674 2.897 4.524
599W W 686 2.808 3.449 3.475
600W W 687 0.373 2.610 5.772
601W W 688 0.766 3.062 5.605
602W W 689 0.126 0.344 3.914
603W W 690 4.035 0.326 1.089
604W W 691 3.920 4.113 4.954
605W W 692 1.639 1.024 4.541
606W W 693 2.306 2.617 5.408
607W W 694 0.249 2.110 2.411
608W W 695 0.585 1.356 4.700
609W W 696 0.636 2.299 3.633
610W W 697 4.260 1.280 1.481
611W W 698 1.432 1.514 4.653
612W W 699 2.609 4.612 0.520
613W W 700 3.661 2.906 5.515
614W W 701 0.827 3.593 1.441
615W W 702 2.910 2.240 0.493
616W W 703 1.385 3.254 4.192
617W W 704 1.206 2.595 5.757
618W W 705 1.954 4.198 4.532
619W W 706 0.530 1.065 2.333
620W W 707 0.431 1.228 3.834
621W W 708 1.124 1.267 5.004
622W W 709 1.229 1.084 1.810
623W W 710 2.329 4.904 5.937
624W W 711 3.953 0.444 1.552
625W W 712 4.046 0.845 4.549
626W W 713 0.139 0.453 3.045
627W W 714 1.843 2.595 4.445
628W W 715 2.074 1.856 4.088
629W W 716 1.144 4.726 4.067
630W W 717 0.774 0.893 5.008
631W W 718 4.879 2.399 2.313
632W W 719 0.606 4.398 3.862
633W W 720 1.243 3.597 4.179
634W W 721 4.789 1.840 1.607
635W W 722 4.892 4.334 1.674
636W W 723 3.486 1.089 3.500
637W W 724 3.307 1.408 5.050
638W W 725 0.307 2.511 4.106
639W W 726 0.263 1.304 0.913
640W W 727 2.931 0.778 0.095
641W W 728 0.540 2.248 5.324
642W W 729 3.764 0.275 0.532
643W W 730 3.602 0.621 2.595
644W W 731 0.698 2.756 2.443
645W W 732 4.064 1.964 4.441
646W W 733 2.457 4.473 1.738
647W W 734 0.022 1.663 5.243
648W W 735 3.665 4.408 3.245
649W W 736 3.615 1.571 4.069
650W W 737 2.771 0.580 3.964
651W W 738 3.999 1.834 2.645
652W W 739 1.897 3.781 0.542
653W W 740 4.256 2.747 2.074
654W W 741 1.963 2.046 4.277
655W W 742 3.355 2.958 1.587
656W W 743 4.762 3.362 1.822
657W W 744 3.445 0.184 2.726
658W W 745 4.482 1.760 3.875
659W W 746 0.397 0.707 1.363
660W W 747 3.978 1.261 3.794
661W W 748 2.890 4.817 0.183
662W W 749 0.525 0.018 4.331
663W W 750 2.062 1.266 2.050
664W W 751 1.910 1.556 0.058
665W W 752 4.278 4.159 0.784
666W W 753 2.518 3.149 0.018
667W W 754 3.451 0.618 0.402
668W W 755 1.108 4.076 2.336
669W W 756 0.410 0.185 0.458
670W W 757 1.979 4.210 1.711
671W W 758 0.919 2.872 0.498
672W W 759 0.047 1.703 2.115
673W W 760 1.768 2.938 0.476
674W W 761 1.782 4.533 2.402
675W W 762 2.714 1.515 4.348
676W W 763 3.548 4.461 0.203
677W W 764 4.416 2.276 1.857
678W W 765 1.162 0.893 4.205
679W W 766 2.976 0.473 4.629
680W W 767 3.113 2.748 5.709
681W W 768 4.779 0.955 0.970
682W W 769 3.239 0.629 3.637
683W W 770 3.147 0.818 1.561
684W W 771 1.796 1.450 4.282
685W W 772 2.279 0.720 2.583
686W W 773 4.423 1.182 3.839
687W W 774 0.323 4.179 2.032
688W W 775 0.448 4.651 0.003
689W W 776 0.629 3.634 1.820
690W W 777 2.985 2.720 4.949
691W W 778 2.261 3.953 1.984
692W W 779 3.723 4.459 1.665
693W W 780 0.884 1.899 4.412
694W W 781 1.469 2.908 4.614
695W W 782 0.326 3.952 4.644
696W W 783 0.415 4.417 5.550
697W W 784 4.789 1.715 4.787
698W W 785 0.578 4.535 3.331
699W W 786 3.340 1.020 0.170
700W W 787 3.251 3.860 1.095
701W W 788 3.665 3.794 2.496
702W W 789 3.344 3.702 2.910
703W W 790 0.044 1.786 2.831
704W W 791 3.155 4.121 0.515
705W W 792 1.895 4.538 2.994
706W W 793 0.616 4.057 1.698
707W W 794 0.791 3.687 3.322
708W W 795 0.362 0.506 4.384
709W W 796 3.235 3.442 1.800
710W W 797 1.094 0.593 3.890
711W W 798 4.069 4.534 3.516
712W W 799 2.338 3.418 1.587
713W W 800 3.927 1.200 4.318
714W W 801 1.931 3.688 0.113
715W W 802 3.287 3.928 1.584
716W W 803 2.379 4.770 1.306
717W W 804 2.744 4.324 0.010
718W W 805 0.456 4.775 1.291
719W W 806 2.707 3.590 3.950
720W W 807 1.469 0.248 2.543
721W W 808 0.882 2.294 2.270
722W W 809 0.741 0.019 3.075
723W W 810 4.453 1.689 1.809
724W W 811 2.318 4.216 4.197
725W W 812 1.741 4.678 3.699
726W W 813 2.219 4.318 0.780
727W W 814 4.154 2.906 4.261
728W W 815 4.822 0.077 2.127
729W W 816 0.603 4.342 2.445
730W W 817 3.037 0.106 5.773
731W W 818 3.653 3.860 1.320
732W W 819 2.028 4.737 0.529
733W W 820 2.161 4.725 5.443
734W W 821 3.245 4.062 2.341
735W W 822 2.925 2.995 0.729
736W W 823 4.575 2.319 3.470
737W W 824 4.233 3.972 3.879
738W W 825 0.019 4.708 3.753
739W W 826 4.236 0.199 4.662
740W W 827 0.495 4.878 3.818
741W W 828 3.765 1.203 5.402
742W W 829 1.129 3.546 5.360
743W W 830 4.351 3.327 1.380
744W W 831 1.163 3.829 4.685
745W W 832 0.539 4.008 5.987
746W W 833 2.789 4.094 2.552
747W W 834 3.911 3.223 5.056
748W W 835 0.858 4.493 2.824
749W W 836 2.566 0.259 5.772
750W W 837 3.243 4.429 3.429
751W W 838 0.093 4.793 4.796
752W W 839 3.404 0.042 4.114
753W W 840 4.209 0.529 3.496
754W W 841 3.485 4.352 5.563
755W W 842 1.699 1.840 5.590
756W W 843 2.412 0.101 5.238
757W W 844 1.674 4.734 0.218
758W W 845 2.747 1.909 5.801
759W W 846 2.950 4.677 4.006
760W W 847 0.296 2.319 4.721
761W W 848 4.955 1.497 5.748
762W W 849 4.901 4.956 1.111
763W W 850 0.181 2.031 5.477
764W W 851 2.593 3.857 5.176
765W W 852 1.453 3.046 3.776
766W W 853 1.050 2.799 2.016
767W W 854 0.124 2.267 0.451
768W W 855 0.595 4.182 4.326
769W W 856 2.775 0.252 1.707
770W W 857 2.055 0.627 5.199
771W W 858 4.235 3.722 4.528
772W W 859 3.956 0.396 2.739
773W W 860 3.245 3.786 0.031
774W W 861 1.514 1.419 3.903
775W W 862 3.791 0.569 5.471
776W W 863 2.155 1.937 5.369
777W W 864 4.605 0.926 5.666
778W W 865 2.501 3.511 4.849
779W W 866 1.617 2.514 0.081
780W W 867 1.880 0.104 0.889
781W W 868 3.987 2.291 1.728
782W W 869 0.091 1.531 0.234
783W W 870 0.901 3.321 4.086
784W W 871 1.307 3.585 3.264
785W W 872 0.570 1.451 2.068
786W W 873 0.758 3.350 3.610
787W W 874 0.573 3.982 5.436
788W W 875 0.766 1.544 0.057
789W W 876 2.703 2.910 5.491
790W W 877 0.375 1.010 4.899
791W W 878 1.786 4.210 3.982
792W W 879 3.118 1.405 1.303
793W W 880 3.336 0.934 5.474
794W W 881 0.971 1.400 2.431
795W W 882 3.038 0.546 2.729
796W W 883 4.790 2.302 2.858
797W W 884 4.500 0.656 1.182
798W W 885 3.412 4.715 2.936
799W W 886 2.393 3.242 1.322
800W W 887 3.437 4.364 1.172
801W W 888 1.498 4.069 0.880
802W W 889 4.602 0.516 0.409
803W W 890 3.495 3.299 5.850
804W W 891 2.486 3.387 0.753
805W W 892 0.552 4.480 0.484
806W W 893 4.142 3.670 3.267
807W W 894 4.342 4.960 1.194
808W W 895 4.692 2.736 3.998
809W W 896 3.559 1.910 4.507
810W W 897 3.501 2.242 1.492
811W W 898 1.078 2.950 4.818
812W W 899 0.277 3.064 2.640
813W W 900 4.286 3.183 3.310
814W W 901 4.027 4.263 0.005
815W W 902 4.160 1.167 2.486
816W W 903 2.700 4.146 4.581
817W W 904 4.706 2.949 0.206
818W W 905 2.441 4.990 0.386
819W W 906 4.450 4.902 3.726
820W W 907 4.205 4.242 2.814
821W W 908 4.573 0.717 3.137
822W W 909 0.615 2.898 3.086
823W W 910 2.791 3.340 0.414
824W W 911 0.628 3.917 3.862
825W W 912 2.287 4.367 5.886
826W W 913 1.987 4.839 4.523
827W W 914 3.615 1.634 2.811
828W W 915 4.482 4.228 0.127
829W W 916 3.567 1.426 0.380
830W W 917 3.860 2.572 3.870
831W W 918 2.574 4.465 3.248
832W W 919 2.479 4.375 3.720
833W W 920 4.291 3.766 0.266
834W W 921 1.896 1.822 1.551
835W W 922 2.803 4.085 3.989
836W W 923 3.532 0.244 2.279
837W W 924 4.173 2.308 3.058
838W W 925 3.979 3.630 4.137
839W W 926 2.535 4.747 2.788
840W W 927 4.774 3.845 4.510
841W W 928 3.444 0.778 2.127
842W W 929 0.352 2.412 2.819
843W W 930 1.034 0.399 0.189
844W W 931 4.728 3.063 3.229
845W W 932 4.282 4.062 2.293
846W W 933 0.709 3.545 0.826
847W W 934 0.220 0.223 1.049
848W W 935 4.848 0.043 4.028
849W W 936 4.969 1.166 2.333
850W W 937 2.058 3.352 3.634
851W W 938 2.697 0.366 0.345
852W W 939 0.217 3.704 2.737
853W W 940 2.163 4.339 5.022
854W W 941 1.855 4.217 1.289
855W W 942 4.571 1.971 4.320
856W W 943 4.330 0.741 1.909
857W W 944 4.123 0.892 5.469
858W W 945 0.707 4.058 0.733
859W W 946 1.994 0.086 4.048
860W W 947 3.668 0.098 1.231
861W W 948 4.468 2.397 2.573
862W W 949 4.189 1.308 4.728
863W W 950 1.473 1.745 4.223
864W W 951 2.427 0.675 0.476
865W W 952 4.353 3.235 4.801
866W W 953 2.040 3.666 4.510
867W W 954 1.403 3.703 3.172
868W W 955 2.293 1.438 4.273
869W W 956 1.656 3.956 4.727
870W W 957 0.088 4.240 2.533
871W W 958 1.076 3.288 2.488
872W W 959 1.343 2.718 1.177
873W W 960 2.959 3.804 1.931
874W W 961 1.297 4.587 4.767
875W W 962 0.728 1.773 2.470
876W W 963 4.619 0.761 2.382
877W W 964 3.855 4.059 0.406
878W W 965 4.703 3.132 0.793
879W W 966 1.956 1.442 3.763
880W W 967 1.022 1.082 3.769
881W W 968 4.574 2.714 5.570
882W W 969 1.359 0.863 0.372
883W W 970 4.685 1.278 0.300
884W W 971 3.840 2.246 0.149
885W W 972 2.276 1.273 5.144
886W W 973 0.330 0.495 5.831
887W W 974 2.462 0.347 4.679
888W W 975 3.018 1.693 4.742
889W W 976 3.826 1.404 1.392
890W W 977 0.115 0.840 2.680
891W W 978 3.089 3.841 5.278
892W W 979 0.626 1.477 0.623
893W W 980 4.637 2.836 1.804
894W W 981 1.570 0.020 1.886
895W W 982 0.408 2.551 3.311
896W W 983 4.846 4.063 2.922
897W W 984 0.461 3.603 5.049
898W W 985 2.488 1.751 1.302
899W W 986 1.589 2.266 5.033
900W W 987 3.371 2.489 0.121
901W W 988 1.154 3.890 0.634
902W W 989 0.545 0.966 1.793
903W W 990 3.053 0.840 3.320
904W W 991 4.179 4.213 1.550
905W W 992 3.358 3.447 3.367
906W W 993 0.902 0.175 5.480
907W W 994 4.697 0.021 5.240
908W W 995 1.638 3.122 1.508
909W W 996 4.158 0.849 2.846
910W W 997 3.810 2.675 0.421
911W W 998 2.606 0.138 2.323
912W W 999 4.004 4.778 5.043
913W W 1000 2.529 1.595 5.486
914W W 1001 3.189 0.260 1.623
915W W 1002 2.642 0.860 2.369
916W W 1003 0.583 0.407 2.066
917W W 1004 2.027 0.982 4.960
918W W 1005 4.067 0.117 5.864
919W W 1006 1.932 0.087 5.334
920W W 1007 4.263 1.581 2.377
921W W 1008 2.848 4.116 5.620
922W W 1009 0.796 0.163 4.707
923W W 1010 0.910 1.776 5.500
924W W 1011 1.997 4.598 4.149
925W W 1012 0.283 2.899 5.420
926W W 1013 3.876 0.203 3.486
927W W 1014 2.356 2.239 5.827
928W W 1015 4.055 2.486 5.514
929W W 1016 2.850 0.935 4.297
930W W 1017 0.701 0.222 5.966
931W W 1018 1.129 1.125 3.029
932W W 1019 4.500 4.775 4.314
933W W 1020 3.933 4.942 1.607
934W W 1021 4.315 2.981 2.494
935W W 1022 3.876 0.243 1.925
936W W 1023 1.783 3.546 1.441
937W W 1024 3.135 1.371 3.961
938W W 1025 4.698 3.620 5.537
939W W 1026 2.681 4.847 1.588
940W W 1027 2.412 0.240 2.775
941W W 1028 2.621 3.976 0.723
942W W 1029 4.175 4.461 4.109
943W W 1030 1.673 3.882 1.885
944W W 1031 3.558 4.898 2.021
945W W 1032 2.586 2.576 4.654
946W W 1033 4.896 1.044 4.059
947W W 1034 4.125 1.365 5.255
948W W 1035 3.544 3.469 1.449
949W W 1036 4.246 1.688 0.565
950W W 1037 1.918 4.140 3.398
951W W 1038 4.742 3.861 2.434
952W W 1039 0.007 1.465 1.284
953W W 1040 3.970 1.590 0.103
954W W 1041 0.036 0.959 0.173
955W W 1042 2.411 2.676 1.078
956W W 1043 3.669 3.920 3.259
957W W 1044 3.422 1.732 3.716
958W W 1045 1.963 0.036 2.037
959W W 1046 4.999 3.491 2.185
960W W 1047 1.724 3.821 3.753
961W W 1048 1.629 3.062 4.454
962W W 1049 0.620 2.232 0.597
963W W 1050 1.189 3.356 3.033
964W W 1051 1.200 2.767 4.143
965W W 1052 0.191 1.539 4.041
966W W 1053 0.132 1.349 4.816
5.00000 5.00000 6.00000
In the top file:
#include "martini_v2.1.itp"
#include "Protein_A.itp"
[ system ]
; name
Martini system from 1UBQ.pdb
[ molecules ]
; name number
Protein_A 1
W 890
As I said the solvated structure looks normal, Ubiquitin is at the center of box surrounded by W. the water density looks even everywhere. I pasted the gro file so maybe people can find sth wrong there.
I am able to run protein alone in vacumm without error for 500000 steps. I am able to run water box alone without error for 116100 steps. But when I run protein in water, something went wrong within a few thousand steps.
I noted in mdp file of protein simulation, I cannot put Protein_A as energygrps. I got error messages when "grompp". Why?
How can I add ions to solvated box? Can you give me an example of gromacs command?
Here is the gro file of protein in water:
Warning: Spoiler!
[ Click to expand ]
[ Click to hide ]
Martini system from 1UBQ.pdb
1053
1MET BB 1 2.152 2.287 1.804
1MET SC1 2 1.987 2.050 2.057
2GLN BB 3 2.121 2.519 1.953
2GLN SC1 4 2.197 2.804 1.709
3ILE BB 5 2.202 2.616 2.253
3ILE SC1 6 2.142 2.371 2.433
4PHE BB 7 2.185 2.911 2.449
4PHE SC1 8 2.053 3.077 2.241
4PHE SC2 9 2.124 3.227 2.027
4PHE SC3 10 1.894 3.086 2.023
5VAL BB 11 2.334 3.056 2.718
5VAL SC1 12 2.489 2.863 2.815
6LYS BB 13 2.299 3.324 2.927
6LYS SC1 14 2.062 3.515 2.910
6LYS SC2 15 1.866 3.685 2.922
7THR BB 16 2.508 3.487 3.156
7THR SC1 17 2.755 3.454 3.084
8LEU BB 18 2.395 3.747 3.326
8LEU SC1 19 2.413 3.638 3.633
9THR BB 20 2.598 4.000 3.158
9THR SC1 21 2.852 3.943 3.157
10GLY BB 22 2.416 3.921 2.850
11LYS BB 23 2.552 3.743 2.720
11LYS SC1 24 2.872 3.737 2.672
11LYS SC2 25 2.983 3.655 2.434
12THR BB 26 2.474 3.484 2.480
12THR SC1 27 2.217 3.500 2.442
13ILE BB 28 2.646 3.219 2.350
13ILE SC1 29 2.844 3.114 2.565
14THR BB 30 2.559 2.957 2.115
14THR SC1 31 2.592 3.061 1.879
15LEU BB 32 2.681 2.614 2.112
15LEU SC1 33 2.713 2.588 2.435
16GLU BB 34 2.645 2.338 1.958
16GLU SC1 35 2.592 2.472 1.598
17VAL BB 36 2.494 2.033 2.113
17VAL SC1 37 2.551 2.095 2.364
18GLU BB 38 2.336 1.734 2.108
18GLU SC1 39 2.386 1.580 1.765
19PRO BB 40 2.108 1.629 2.321
19PRO SC1 41 1.855 1.567 2.177
20SER BB 42 2.336 1.352 2.431
20SER SC1 43 2.403 1.231 2.219
21ASP BB 44 2.553 1.580 2.566
21ASP SC1 45 2.767 1.623 2.347
22THR BB 46 2.659 1.545 2.857
22THR SC1 47 2.816 1.344 2.904
23ILE BB 48 2.728 1.795 3.142
23ILE SC1 49 2.442 1.915 3.153
24GLU BB 50 3.022 1.778 3.101
24GLU SC1 51 3.165 1.462 3.267
25ASN BB 52 3.008 1.880 2.758
25ASN SC1 53 3.194 1.693 2.611
26VAL BB 54 2.881 2.170 2.814
26VAL SC1 55 2.627 2.243 2.825
27LYS BB 56 3.126 2.267 3.027
27LYS SC1 57 2.967 2.211 3.313
27LYS SC2 58 2.783 2.222 3.513
28ALA BB 59 3.382 2.220 2.800
29LYS BB 60 3.250 2.425 2.551
29LYS SC1 61 3.075 2.236 2.370
29LYS SC2 62 3.013 2.034 2.206
30ILE BB 63 3.243 2.684 2.749
30ILE SC1 64 2.952 2.707 2.855
31GLN BB 65 3.560 2.701 2.817
31GLN SC1 66 3.791 2.493 3.044
32ASP BB 67 3.675 2.724 2.500
32ASP SC1 68 3.727 2.434 2.395
33LYS BB 69 3.504 3.009 2.436
33LYS SC1 70 3.230 2.894 2.296
33LYS SC2 71 3.069 2.953 2.091
34GLU BB 72 3.625 3.197 2.700
34GLU SC1 73 3.252 3.339 2.727
35GLY BB 74 3.723 3.099 3.039
36ILE BB 75 3.485 2.948 3.242
36ILE SC1 76 3.235 3.117 3.172
37PRO BB 77 3.555 2.721 3.420
37PRO SC1 78 3.828 2.762 3.540
38PRO BB 79 3.438 2.418 3.543
38PRO SC1 80 3.502 2.209 3.344
39ASP BB 81 3.325 2.472 3.812
39ASP SC1 82 3.530 2.512 4.056
40GLN BB 83 3.163 2.756 3.793
40GLN SC1 84 3.480 2.980 3.848
41GLN BB 85 2.937 2.747 3.670
41GLN SC1 86 3.064 2.672 3.314
42ARG BB 87 2.624 2.654 3.713
42ARG SC1 88 2.531 2.743 4.000
42ARG SC2 89 2.248 2.813 4.159
43LEU BB 90 2.359 2.566 3.516
43LEU SC1 91 2.522 2.526 3.231
44ILE BB 92 2.002 2.618 3.516
44ILE SC1 93 1.972 2.819 3.750
45PHE BB 94 1.743 2.570 3.342
45PHE SC1 95 1.640 2.429 3.103
45PHE SC2 96 1.467 2.224 3.068
45PHE SC3 97 1.413 2.466 2.960
46ALA BB 98 1.396 2.573 3.501
47GLY BB 99 1.515 2.604 3.793
48LYS BB 100 1.723 2.291 3.791
48LYS SC1 101 1.471 2.107 3.720
48LYS SC2 102 1.334 2.030 3.500
49GLN BB 103 2.028 2.173 3.789
49GLN SC1 104 2.283 2.307 4.051
50LEU BB 105 2.244 2.084 3.578
50LEU SC1 106 2.084 2.197 3.305
51GLU BB 107 2.444 1.810 3.630
51GLU SC1 108 2.329 1.547 3.903
52ASP BB 109 2.743 1.594 3.595
52ASP SC1 110 2.983 1.790 3.636
53GLY BB 111 2.663 1.364 3.386
54ARG BB 112 2.378 1.448 3.283
54ARG SC1 113 2.181 1.313 3.489
54ARG SC2 114 2.226 1.007 3.567
55THR BB 115 2.206 1.433 2.962
55THR SC1 116 2.252 1.188 2.887
56LEU BB 117 2.064 1.667 2.829
56LEU SC1 118 2.255 1.903 2.705
57SER BB 119 1.782 1.450 2.694
57SER SC1 120 1.857 1.248 2.576
58ASP BB 121 1.644 1.431 3.001
58ASP SC1 122 1.808 1.215 3.168
59TYR BB 123 1.547 1.744 3.042
59TYR SC1 124 1.740 1.833 3.257
59TYR SC2 125 1.801 1.800 3.518
59TYR SC3 126 1.979 1.729 3.328
60ASN BB 127 1.447 1.837 2.731
60ASN SC1 128 1.169 1.718 2.690
61ILE BB 129 1.691 1.949 2.562
61ILE SC1 130 1.840 2.113 2.779
62GLN BB 131 1.551 2.064 2.277
62GLN SC1 132 1.179 1.974 2.233
63LYS BB 133 1.607 2.348 2.062
63LYS SC1 134 1.576 2.217 1.774
63LYS SC2 135 1.381 2.270 1.590
64GLU BB 136 1.646 2.659 2.083
64GLU SC1 137 1.684 2.704 1.693
65SER BB 138 1.731 2.688 2.438
65SER SC1 139 1.655 2.481 2.542
66THR BB 140 1.797 2.883 2.786
66THR SC1 141 1.805 3.134 2.718
67LEU BB 142 2.047 2.773 3.004
67LEU SC1 143 2.142 2.487 2.909
68HIS BB 144 2.226 2.960 3.239
68HIS SC1 145 1.974 3.118 3.324
68HIS SC2 146 1.714 3.070 3.273
68HIS SC3 147 1.802 3.324 3.295
69LEU BB 148 2.482 3.055 3.415
69LEU SC1 149 2.736 2.997 3.234
70VAL BB 150 2.582 3.160 3.723
70VAL SC1 151 2.360 3.194 3.863
71LEU BB 152 2.884 3.175 3.914
71LEU SC1 153 3.083 3.238 3.658
72ARG BB 154 3.068 3.054 4.190
72ARG SC1 155 2.995 2.749 4.256
72ARG SC2 156 2.923 2.450 4.126
73LEU BB 157 3.329 3.153 4.300
73LEU SC1 158 3.412 3.409 4.107
74ARG BB 159 3.571 3.093 4.473
74ARG SC1 160 3.635 2.778 4.489
74ARG SC2 161 3.899 2.590 4.408
75GLY BB 162 3.664 3.309 4.689
76GLY BB 163 3.500 3.545 4.915
77W W 164 3.047 1.499 1.968
78W W 165 1.142 1.573 1.846
79W W 166 2.768 1.197 5.465
80W W 167 3.487 4.695 0.764
81W W 168 0.340 3.819 1.422
82W W 169 1.460 3.839 0.236
83W W 170 0.944 3.320 0.294
84W W 171 3.694 2.328 1.393
85W W 172 3.051 1.355 1.461
86W W 173 0.634 2.079 1.950
87W W 174 0.857 2.175 3.210
88W W 175 2.651 3.496 1.875
89W W 176 3.719 1.104 1.895
90W W 177 2.236 2.217 1.157
91W W 178 1.595 1.440 1.735
92W W 179 2.991 0.117 2.646
93W W 180 2.937 4.745 5.543
94W W 181 3.450 1.639 1.566
95W W 182 3.496 3.677 2.117
96W W 183 0.286 1.101 5.328
97W W 184 1.680 1.470 1.502
98W W 185 3.453 0.918 0.840
99W W 186 3.546 1.811 4.681
100W W 187 1.276 1.352 0.456
101W W 188 2.381 1.221 0.220
102W W 189 2.864 3.087 1.557
103W W 190 1.308 1.555 1.948
104W W 191 3.434 4.738 3.825
105W W 192 4.369 3.940 1.819
106W W 193 4.513 3.616 4.145
107W W 194 3.509 1.804 5.844
108W W 195 2.360 3.121 4.554
109W W 196 2.395 1.724 0.099
110W W 197 1.908 1.940 1.431
111W W 198 3.258 2.675 4.525
112W W 199 3.876 3.335 5.588
113W W 200 4.765 3.189 4.006
114W W 201 1.584 2.062 0.209
115W W 202 3.546 2.657 1.907
116W W 203 3.028 2.266 4.785
117W W 204 3.623 0.215 5.678
118W W 205 4.795 4.106 5.470
119W W 206 3.841 2.685 5.863
120W W 207 4.675 0.240 4.873
121W W 208 2.099 2.856 5.824
122W W 209 1.976 3.571 4.398
123W W 210 1.578 0.061 5.746
124W W 211 1.612 4.299 5.498
125W W 212 2.731 2.336 5.178
126W W 213 0.200 2.837 1.474
127W W 214 3.218 2.346 5.279
128W W 215 1.592 2.115 4.217
129W W 216 1.286 2.043 5.771
130W W 217 0.695 3.916 1.139
131W W 218 2.308 1.262 5.695
132W W 219 4.155 1.174 0.963
133W W 220 3.468 2.801 5.120
134W W 221 1.715 2.034 4.730
135W W 222 1.318 3.688 2.418
136W W 223 4.483 0.750 5.123
137W W 224 2.230 0.074 3.649
138W W 225 2.867 1.290 4.196
139W W 226 1.447 3.942 5.202
140W W 227 2.599 2.079 4.661
141W W 228 0.833 0.014 1.345
142W W 229 3.486 1.777 5.308
143W W 230 1.864 0.415 1.765
144W W 231 0.180 3.064 1.933
145W W 232 4.782 4.181 0.994
146W W 233 1.757 0.469 0.721
147W W 234 1.490 3.104 5.105
148W W 235 3.669 3.508 1.601
149W W 236 3.707 3.601 0.552
150W W 237 4.382 3.363 2.191
151W W 238 0.798 1.757 1.151
152W W 239 1.057 2.253 5.449
153W W 240 0.871 1.352 4.218
154W W 241 3.788 1.336 3.231
155W W 242 1.306 1.823 4.580
156W W 243 0.877 1.045 0.597
157W W 244 0.002 4.174 0.586
158W W 245 2.964 1.873 1.414
159W W 246 3.341 1.243 4.529
160W W 247 3.188 3.108 4.813
161W W 248 0.148 0.584 5.437
162W W 249 2.617 2.135 4.517
163W W 250 1.034 3.332 2.009
164W W 251 0.587 4.881 2.614
165W W 252 3.141 2.762 1.534
166W W 253 1.082 3.905 3.825
167W W 254 1.600 4.450 4.430
168W W 255 1.578 3.581 1.980
169W W 256 4.747 2.785 1.199
170W W 257 2.677 4.903 3.617
171W W 258 0.005 1.514 3.551
172W W 259 3.300 3.529 4.511
173W W 260 0.979 3.827 2.859
174W W 261 3.719 4.029 1.836
175W W 262 3.897 0.902 3.391
176W W 263 2.320 2.933 1.295
177W W 264 3.029 0.843 0.562
178W W 265 0.526 4.110 2.787
179W W 266 3.316 3.267 1.298
180W W 267 1.343 3.129 2.346
181W W 268 2.122 0.167 1.482
182W W 269 1.506 3.387 4.633
183W W 270 3.830 4.765 2.910
184W W 271 1.326 1.535 5.474
185W W 272 1.016 3.874 5.661
186W W 273 1.859 3.416 4.968
187W W 274 3.699 1.744 3.351
188W W 275 2.947 4.349 4.857
189W W 276 1.563 3.055 1.339
190W W 277 4.438 3.327 0.252
191W W 278 1.649 2.949 5.896
192W W 279 2.639 2.054 4.016
193W W 280 3.471 1.634 4.235
194W W 281 2.784 3.641 3.881
195W W 282 1.407 0.980 5.563
196W W 283 3.072 3.870 3.531
197W W 284 0.887 1.734 4.937
198W W 285 1.377 4.508 3.550
199W W 286 1.559 0.628 0.063
200W W 287 3.081 2.504 2.025
201W W 288 2.164 4.168 5.469
202W W 289 2.143 1.187 1.592
203W W 290 3.239 2.268 1.021
204W W 291 1.651 1.555 4.343
205W W 292 3.511 4.329 4.769
206W W 293 1.532 0.046 3.660
207W W 294 3.967 0.910 1.579
208W W 295 3.064 1.646 1.941
209W W 296 3.647 1.157 5.918
210W W 297 1.082 1.659 0.749
211W W 298 4.541 0.430 5.574
212W W 299 3.289 4.796 1.282
213W W 300 1.539 1.429 2.333
214W W 301 4.384 1.896 4.890
215W W 302 4.230 2.996 5.789
216W W 303 3.325 4.443 4.266
217W W 304 2.093 3.351 0.972
218W W 305 1.262 0.745 3.491
219W W 306 1.069 2.129 3.835
220W W 307 1.321 0.415 1.064
221W W 308 1.888 1.099 1.099
222W W 309 3.580 1.142 2.489
223W W 310 4.540 0.290 1.581
224W W 311 2.798 0.721 5.678
225W W 312 0.571 4.609 1.746
226W W 313 0.857 4.613 1.006
227W W 314 2.088 2.351 4.765
228W W 315 3.495 1.424 0.854
229W W 316 4.754 2.360 4.732
230W W 317 0.942 3.814 0.256
231W W 318 0.203 1.876 4.781
232W W 319 0.723 0.871 5.765
233W W 320 0.508 4.591 5.121
234W W 321 0.277 4.294 0.982
235W W 322 3.729 2.151 1.859
236W W 323 3.377 2.197 0.534
237W W 324 0.785 2.280 5.879
238W W 325 2.151 1.789 4.668
239W W 326 4.616 0.073 2.582
240W W 327 3.731 3.568 3.629
241W W 328 1.729 0.470 4.201
242W W 329 1.444 1.369 3.637
243W W 330 1.863 2.815 5.428
244W W 331 2.550 4.564 4.414
245W W 332 4.412 2.541 5.223
246W W 333 4.168 1.913 3.522
247W W 334 3.509 4.742 5.008
248W W 335 1.788 3.571 1.492
249W W 336 0.045 2.778 2.877
250W W 337 4.845 3.134 2.773
251W W 338 2.943 1.005 4.751
252W W 339 1.260 0.622 1.557
253W W 340 4.803 2.569 0.716
254W W 341 0.130 4.530 4.378
255W W 342 3.123 1.464 5.701
256W W 343 3.420 1.869 2.032
257W W 344 3.431 1.374 2.226
258W W 345 3.451 1.797 2.313
259W W 346 1.998 0.340 5.875
260W W 347 2.906 0.661 5.206
261W W 348 2.200 1.342 4.206
262W W 349 0.633 0.269 5.091
263W W 350 1.370 3.425 0.231
264W W 351 0.021 2.985 3.662
265W W 352 3.262 0.342 0.060
266W W 353 4.701 2.998 5.275
267W W 354 0.484 2.863 1.156
268W W 355 1.462 3.045 1.976
269W W 356 3.008 0.964 1.178
270W W 357 4.339 0.881 0.529
271W W 358 0.060 3.849 3.387
272W W 359 1.825 3.803 1.087
273W W 360 4.705 2.050 0.163
274W W 361 3.685 3.466 3.443
275W W 362 0.159 3.876 5.295
276W W 363 2.479 1.114 1.226
277W W 364 1.806 3.727 3.931
278W W 365 4.297 1.625 1.091
279W W 366 3.283 2.231 1.618
280W W 367 3.620 1.563 3.688
281W W 368 1.455 3.399 5.765
282W W 369 3.927 3.201 3.808
283W W 370 3.638 4.496 2.127
284W W 371 0.893 2.509 4.000
285W W 372 3.914 1.824 5.559
286W W 373 4.642 1.119 1.820
287W W 374 1.285 2.649 5.235
288W W 375 1.903 3.340 5.476
289W W 376 0.793 4.308 5.788
290W W 377 2.521 1.346 4.665
291W W 378 4.306 4.777 2.876
292W W 379 4.386 1.685 5.423
293W W 380 3.514 1.810 0.657
294W W 381 0.098 2.141 5.973
295W W 382 3.115 4.560 2.263
296W W 383 3.433 0.880 4.875
297W W 384 3.018 0.584 1.899
298W W 385 3.090 0.018 3.758
299W W 386 2.236 3.768 0.939
300W W 387 1.317 3.000 3.724
301W W 388 3.089 1.772 0.640
302W W 389 3.643 4.860 3.385
303W W 390 4.387 4.409 5.415
304W W 391 0.930 0.201 2.243
305W W 392 1.446 1.532 0.921
306W W 393 1.921 0.929 2.313
307W W 394 1.448 4.867 5.395
308W W 395 4.398 4.776 2.226
309W W 396 4.284 2.367 4.149
310W W 397 4.265 3.387 5.254
311W W 398 4.945 0.711 4.719
312W W 399 1.831 4.615 5.784
313W W 400 0.381 1.156 0.442
314W W 401 2.409 0.818 5.969
315W W 402 3.958 0.398 4.333
316W W 403 1.220 2.586 2.536
317W W 404 3.981 1.153 0.355
318W W 405 3.175 3.106 5.429
319W W 406 4.861 2.907 2.262
320W W 407 0.534 3.494 0.030
321W W 408 3.001 1.692 4.527
322W W 409 1.617 1.070 3.536
323W W 410 0.021 4.689 0.409
324W W 411 4.825 1.340 3.129
325W W 412 1.386 0.702 2.804
326W W 413 2.856 3.754 0.384
327W W 414 1.759 1.409 0.641
328W W 415 1.914 2.408 5.737
329W W 416 0.701 3.322 3.003
330W W 417 4.684 0.251 3.169
331W W 418 4.437 4.376 3.183
332W W 419 4.891 4.490 5.329
333W W 420 1.186 4.695 5.874
334W W 421 2.831 3.191 1.517
335W W 422 4.709 4.700 0.017
336W W 423 1.244 4.753 1.983
337W W 424 3.781 4.387 3.925
338W W 425 4.116 0.047 2.483
339W W 426 3.995 3.644 1.940
340W W 427 2.910 4.225 1.497
341W W 428 3.668 2.942 1.524
342W W 429 4.177 2.123 5.266
343W W 430 2.155 3.395 5.895
344W W 431 4.934 3.653 0.960
345W W 432 3.974 4.648 5.765
346W W 433 4.622 4.361 2.123
347W W 434 2.553 0.107 0.853
348W W 435 1.969 3.343 4.144
349W W 436 1.860 3.067 4.263
350W W 437 4.715 1.394 4.453
351W W 438 3.622 3.821 5.705
352W W 439 4.291 1.642 3.135
353W W 440 2.671 2.592 4.535
354W W 441 4.438 1.310 5.773
355W W 442 0.368 3.385 1.456
356W W 443 4.866 3.627 1.394
357W W 444 2.454 1.041 3.210
358W W 445 4.745 0.661 3.670
359W W 446 2.608 1.830 0.461
360W W 447 3.658 2.272 0.856
361W W 448 3.395 2.182 4.410
362W W 449 0.580 3.221 2.092
363W W 450 1.574 3.869 5.810
364W W 451 3.538 0.490 1.743
365W W 452 0.072 0.829 1.921
366W W 453 4.970 2.906 5.729
367W W 454 3.043 2.732 1.200
368W W 455 4.481 0.164 5.921
369W W 456 2.106 4.600 3.451
370W W 457 3.944 3.032 1.854
371W W 458 1.520 1.903 1.251
372W W 459 1.808 2.689 4.119
373W W 460 0.820 3.653 2.279
374W W 461 4.788 3.505 5.007
375W W 462 4.220 2.799 0.163
376W W 463 4.062 3.500 2.738
377W W 464 3.583 0.236 4.594
378W W 465 0.181 3.367 5.367
379W W 466 3.964 4.823 0.237
380W W 467 0.949 2.615 3.284
381W W 468 1.465 3.561 2.344
382W W 469 3.925 1.861 1.078
383W W 470 4.517 3.873 1.356
384W W 471 1.379 0.003 1.227
385W W 472 3.049 2.336 1.700
386W W 473 4.868 4.659 2.479
387W W 474 2.602 2.406 0.810
388W W 475 0.321 4.828 2.209
389W W 476 1.312 2.727 0.323
390W W 477 2.555 0.554 1.063
391W W 478 4.500 1.215 3.407
392W W 479 1.863 3.848 5.396
393W W 480 3.899 1.558 1.893
394W W 481 0.454 2.108 1.378
395W W 482 2.042 0.821 3.171
396W W 483 3.942 1.749 4.931
397W W 484 4.055 0.580 4.917
398W W 485 1.530 0.491 2.074
399W W 486 2.453 1.282 4.717
400W W 487 0.594 2.861 0.199
401W W 488 3.067 4.312 0.903
402W W 489 1.514 0.130 4.890
403W W 490 1.628 2.649 4.694
404W W 491 0.434 3.845 2.366
405W W 492 1.513 4.659 0.634
406W W 493 2.587 0.696 1.512
407W W 494 3.160 3.405 1.765
408W W 495 4.700 4.049 3.891
409W W 496 2.860 0.214 3.357
410W W 497 0.811 3.212 1.136
411W W 498 2.450 4.171 0.347
412W W 499 0.007 3.621 0.008
413W W 500 1.742 4.622 5.059
414W W 501 2.638 0.119 4.182
415W W 502 3.987 4.647 4.607
416W W 503 0.646 1.345 3.336
417W W 504 4.445 3.917 5.822
418W W 505 2.977 0.974 2.712
419W W 506 1.818 2.797 1.307
420W W 507 0.079 2.037 3.438
421W W 508 4.763 1.237 5.017
422W W 509 0.052 0.129 2.659
423W W 510 3.089 0.502 0.920
424W W 511 2.922 1.155 1.759
425W W 512 2.917 1.838 1.536
426W W 513 2.171 1.568 0.569
427W W 514 1.973 0.832 0.536
428W W 515 1.446 0.049 0.781
429W W 516 2.697 0.978 3.757
430W W 517 2.255 4.212 2.592
431W W 518 1.265 4.100 3.459
432W W 519 3.468 4.968 0.012
433W W 520 4.799 3.523 2.989
434W W 521 1.170 0.234 3.479
435W W 522 0.247 0.562 3.521
436W W 523 0.188 1.109 3.417
437W W 524 3.139 0.094 0.544
438W W 525 4.207 0.219 5.256
439W W 526 3.124 4.375 5.340
440W W 527 3.274 0.221 4.900
441W W 528 1.118 4.889 4.486
442W W 529 1.126 0.599 5.672
443W W 530 0.931 4.800 5.180
444W W 531 2.527 1.764 4.286
445W W 532 0.207 0.029 5.246
446W W 533 3.265 0.913 4.146
447W W 534 4.978 0.884 1.392
448W W 535 3.811 0.754 1.006
449W W 536 4.331 4.872 5.613
450W W 537 1.113 1.766 0.288
451W W 538 0.208 3.887 0.276
452W W 539 4.000 3.952 5.541
453W W 540 0.007 3.432 3.395
454W W 541 3.821 3.655 0.978
455W W 542 1.585 1.715 5.144
456W W 543 0.162 2.704 0.193
457W W 544 0.945 4.969 0.672
458W W 545 2.898 4.990 2.025
459W W 546 4.113 3.078 0.495
460W W 547 2.367 2.855 0.626
461W W 548 0.898 4.727 0.256
462W W 549 1.067 4.590 3.234
463W W 550 0.587 0.371 2.510
464W W 551 2.889 4.558 1.211
465W W 552 1.132 0.657 2.070
466W W 553 1.656 0.678 4.976
467W W 554 1.133 2.238 0.939
468W W 555 2.004 1.861 4.879
469W W 556 4.554 0.184 0.873
470W W 557 0.636 0.669 0.553
471W W 558 4.975 0.845 5.154
472W W 559 0.047 2.549 3.703
473W W 560 0.285 0.029 3.163
474W W 561 4.130 2.206 2.191
475W W 562 2.774 2.311 1.207
476W W 563 2.011 1.339 4.720
477W W 564 4.651 4.275 4.366
478W W 565 4.009 0.794 0.015
479W W 566 1.014 0.447 4.293
480W W 567 4.243 2.546 4.638
481W W 568 2.284 1.151 0.835
482W W 569 2.726 1.203 0.540
483W W 570 0.060 0.678 0.518
484W W 571 2.569 4.511 5.593
485W W 572 1.788 1.123 5.782
486W W 573 4.451 3.811 5.108
487W W 574 2.033 0.156 0.461
488W W 575 1.147 2.426 4.581
489W W 576 2.324 0.893 4.399
490W W 577 3.548 1.855 1.862
491W W 578 0.270 3.998 4.096
492W W 579 0.833 0.491 1.697
493W W 580 0.346 1.670 5.846
494W W 581 0.710 0.338 0.888
495W W 582 3.673 0.525 3.739
496W W 583 3.651 4.156 4.275
497W W 584 0.890 4.477 4.533
498W W 585 2.809 3.842 1.248
499W W 586 1.198 2.096 5.085
500W W 587 2.487 2.226 0.368
501W W 588 3.174 1.970 4.116
502W W 589 0.934 4.247 1.284
503W W 590 0.683 1.581 1.668
504W W 591 0.516 3.343 4.466
505W W 592 4.450 2.455 0.486
506W W 593 0.168 4.393 2.938
507W W 594 0.165 2.598 1.935
508W W 595 3.342 3.937 4.018
509W W 596 0.196 2.268 1.018
510W W 597 4.923 0.158 0.167
511W W 598 4.849 2.243 1.450
512W W 599 4.935 0.068 5.670
513W W 600 1.305 4.114 1.564
514W W 601 3.554 4.522 2.586
515W W 602 1.628 2.326 1.226
516W W 603 3.242 4.137 2.794
517W W 604 2.062 0.466 3.553
518W W 605 1.365 4.726 2.718
519W W 606 4.557 0.896 0.132
520W W 607 2.958 1.439 0.116
521W W 608 4.900 3.236 4.547
522W W 609 1.142 4.556 1.578
523W W 610 3.764 3.278 0.174
524W W 611 2.014 0.624 4.492
525W W 612 4.898 0.424 1.230
526W W 613 4.798 3.828 0.462
527W W 614 0.534 1.816 3.305
528W W 615 4.108 4.621 0.986
529W W 616 0.358 3.435 3.859
530W W 617 0.963 2.697 2.853
531W W 618 0.806 0.467 2.973
532W W 619 0.207 3.322 0.492
533W W 620 4.553 1.840 2.644
534W W 621 4.791 4.415 3.409
535W W 622 1.943 0.818 1.442
536W W 623 1.393 4.079 4.304
537W W 624 4.603 2.883 3.591
538W W 625 1.638 4.787 1.524
539W W 626 2.208 3.501 1.748
540W W 627 0.469 1.130 2.827
541W W 628 4.321 4.645 1.615
542W W 629 1.061 0.814 1.219
543W W 630 0.093 0.170 1.606
544W W 631 3.157 3.574 0.655
545W W 632 4.730 4.761 1.702
546W W 633 1.472 0.957 2.147
547W W 634 4.518 0.501 4.306
548W W 635 3.473 2.434 4.512
549W W 636 0.724 4.020 4.989
550W W 637 0.769 2.493 1.784
551W W 638 4.905 2.492 5.386
552W W 639 1.654 0.604 3.129
553W W 640 3.856 2.828 1.172
554W W 641 3.378 1.097 3.004
555W W 642 4.305 1.857 5.888
556W W 643 3.388 2.594 2.041
557W W 644 2.298 0.488 3.991
558W W 645 1.159 1.678 3.459
559W W 646 1.349 2.367 4.551
560W W 647 2.062 0.484 2.272
561W W 648 1.435 3.056 1.815
562W W 649 3.844 0.033 3.944
563W W 650 0.924 1.158 0.122
564W W 651 3.340 0.246 3.261
565W W 652 0.585 0.858 0.951
566W W 653 0.948 1.918 1.655
567W W 654 1.324 3.436 1.296
568W W 655 2.565 2.755 0.160
569W W 656 0.106 1.283 1.763
570W W 657 1.935 0.903 4.097
571W W 658 0.633 1.493 5.192
572W W 659 0.670 1.788 3.981
573W W 660 0.320 4.769 0.836
574W W 661 0.345 2.075 4.303
575W W 662 1.365 0.326 0.448
576W W 663 1.121 1.378 1.414
577W W 664 2.693 3.581 4.405
578W W 665 2.184 3.005 4.600
579W W 666 4.220 2.424 1.151
580W W 667 0.839 0.815 3.366
581W W 668 4.187 0.588 2.406
582W W 669 1.233 3.061 5.567
583W W 670 3.480 3.282 0.843
584W W 671 2.930 3.308 4.513
585W W 672 4.775 4.737 3.030
586W W 673 0.221 4.318 4.971
587W W 674 3.016 2.995 0.283
588W W 675 1.831 2.142 0.711
589W W 676 4.694 4.150 4.996
590W W 677 4.979 2.856 4.737
591W W 678 4.779 2.045 0.782
592W W 679 1.506 1.969 4.717
593W W 680 2.718 3.753 5.908
594W W 681 1.621 4.101 2.925
595W W 682 1.286 1.724 4.032
596W W 683 4.597 2.109 5.568
597W W 684 0.742 0.726 4.492
598W W 685 0.674 2.897 4.524
599W W 686 2.808 3.449 3.475
600W W 687 0.373 2.610 5.772
601W W 688 0.766 3.062 5.605
602W W 689 0.126 0.344 3.914
603W W 690 4.035 0.326 1.089
604W W 691 3.920 4.113 4.954
605W W 692 1.639 1.024 4.541
606W W 693 2.306 2.617 5.408
607W W 694 0.249 2.110 2.411
608W W 695 0.585 1.356 4.700
609W W 696 0.636 2.299 3.633
610W W 697 4.260 1.280 1.481
611W W 698 1.432 1.514 4.653
612W W 699 2.609 4.612 0.520
613W W 700 3.661 2.906 5.515
614W W 701 0.827 3.593 1.441
615W W 702 2.910 2.240 0.493
616W W 703 1.385 3.254 4.192
617W W 704 1.206 2.595 5.757
618W W 705 1.954 4.198 4.532
619W W 706 0.530 1.065 2.333
620W W 707 0.431 1.228 3.834
621W W 708 1.124 1.267 5.004
622W W 709 1.229 1.084 1.810
623W W 710 2.329 4.904 5.937
624W W 711 3.953 0.444 1.552
625W W 712 4.046 0.845 4.549
626W W 713 0.139 0.453 3.045
627W W 714 1.843 2.595 4.445
628W W 715 2.074 1.856 4.088
629W W 716 1.144 4.726 4.067
630W W 717 0.774 0.893 5.008
631W W 718 4.879 2.399 2.313
632W W 719 0.606 4.398 3.862
633W W 720 1.243 3.597 4.179
634W W 721 4.789 1.840 1.607
635W W 722 4.892 4.334 1.674
636W W 723 3.486 1.089 3.500
637W W 724 3.307 1.408 5.050
638W W 725 0.307 2.511 4.106
639W W 726 0.263 1.304 0.913
640W W 727 2.931 0.778 0.095
641W W 728 0.540 2.248 5.324
642W W 729 3.764 0.275 0.532
643W W 730 3.602 0.621 2.595
644W W 731 0.698 2.756 2.443
645W W 732 4.064 1.964 4.441
646W W 733 2.457 4.473 1.738
647W W 734 0.022 1.663 5.243
648W W 735 3.665 4.408 3.245
649W W 736 3.615 1.571 4.069
650W W 737 2.771 0.580 3.964
651W W 738 3.999 1.834 2.645
652W W 739 1.897 3.781 0.542
653W W 740 4.256 2.747 2.074
654W W 741 1.963 2.046 4.277
655W W 742 3.355 2.958 1.587
656W W 743 4.762 3.362 1.822
657W W 744 3.445 0.184 2.726
658W W 745 4.482 1.760 3.875
659W W 746 0.397 0.707 1.363
660W W 747 3.978 1.261 3.794
661W W 748 2.890 4.817 0.183
662W W 749 0.525 0.018 4.331
663W W 750 2.062 1.266 2.050
664W W 751 1.910 1.556 0.058
665W W 752 4.278 4.159 0.784
666W W 753 2.518 3.149 0.018
667W W 754 3.451 0.618 0.402
668W W 755 1.108 4.076 2.336
669W W 756 0.410 0.185 0.458
670W W 757 1.979 4.210 1.711
671W W 758 0.919 2.872 0.498
672W W 759 0.047 1.703 2.115
673W W 760 1.768 2.938 0.476
674W W 761 1.782 4.533 2.402
675W W 762 2.714 1.515 4.348
676W W 763 3.548 4.461 0.203
677W W 764 4.416 2.276 1.857
678W W 765 1.162 0.893 4.205
679W W 766 2.976 0.473 4.629
680W W 767 3.113 2.748 5.709
681W W 768 4.779 0.955 0.970
682W W 769 3.239 0.629 3.637
683W W 770 3.147 0.818 1.561
684W W 771 1.796 1.450 4.282
685W W 772 2.279 0.720 2.583
686W W 773 4.423 1.182 3.839
687W W 774 0.323 4.179 2.032
688W W 775 0.448 4.651 0.003
689W W 776 0.629 3.634 1.820
690W W 777 2.985 2.720 4.949
691W W 778 2.261 3.953 1.984
692W W 779 3.723 4.459 1.665
693W W 780 0.884 1.899 4.412
694W W 781 1.469 2.908 4.614
695W W 782 0.326 3.952 4.644
696W W 783 0.415 4.417 5.550
697W W 784 4.789 1.715 4.787
698W W 785 0.578 4.535 3.331
699W W 786 3.340 1.020 0.170
700W W 787 3.251 3.860 1.095
701W W 788 3.665 3.794 2.496
702W W 789 3.344 3.702 2.910
703W W 790 0.044 1.786 2.831
704W W 791 3.155 4.121 0.515
705W W 792 1.895 4.538 2.994
706W W 793 0.616 4.057 1.698
707W W 794 0.791 3.687 3.322
708W W 795 0.362 0.506 4.384
709W W 796 3.235 3.442 1.800
710W W 797 1.094 0.593 3.890
711W W 798 4.069 4.534 3.516
712W W 799 2.338 3.418 1.587
713W W 800 3.927 1.200 4.318
714W W 801 1.931 3.688 0.113
715W W 802 3.287 3.928 1.584
716W W 803 2.379 4.770 1.306
717W W 804 2.744 4.324 0.010
718W W 805 0.456 4.775 1.291
719W W 806 2.707 3.590 3.950
720W W 807 1.469 0.248 2.543
721W W 808 0.882 2.294 2.270
722W W 809 0.741 0.019 3.075
723W W 810 4.453 1.689 1.809
724W W 811 2.318 4.216 4.197
725W W 812 1.741 4.678 3.699
726W W 813 2.219 4.318 0.780
727W W 814 4.154 2.906 4.261
728W W 815 4.822 0.077 2.127
729W W 816 0.603 4.342 2.445
730W W 817 3.037 0.106 5.773
731W W 818 3.653 3.860 1.320
732W W 819 2.028 4.737 0.529
733W W 820 2.161 4.725 5.443
734W W 821 3.245 4.062 2.341
735W W 822 2.925 2.995 0.729
736W W 823 4.575 2.319 3.470
737W W 824 4.233 3.972 3.879
738W W 825 0.019 4.708 3.753
739W W 826 4.236 0.199 4.662
740W W 827 0.495 4.878 3.818
741W W 828 3.765 1.203 5.402
742W W 829 1.129 3.546 5.360
743W W 830 4.351 3.327 1.380
744W W 831 1.163 3.829 4.685
745W W 832 0.539 4.008 5.987
746W W 833 2.789 4.094 2.552
747W W 834 3.911 3.223 5.056
748W W 835 0.858 4.493 2.824
749W W 836 2.566 0.259 5.772
750W W 837 3.243 4.429 3.429
751W W 838 0.093 4.793 4.796
752W W 839 3.404 0.042 4.114
753W W 840 4.209 0.529 3.496
754W W 841 3.485 4.352 5.563
755W W 842 1.699 1.840 5.590
756W W 843 2.412 0.101 5.238
757W W 844 1.674 4.734 0.218
758W W 845 2.747 1.909 5.801
759W W 846 2.950 4.677 4.006
760W W 847 0.296 2.319 4.721
761W W 848 4.955 1.497 5.748
762W W 849 4.901 4.956 1.111
763W W 850 0.181 2.031 5.477
764W W 851 2.593 3.857 5.176
765W W 852 1.453 3.046 3.776
766W W 853 1.050 2.799 2.016
767W W 854 0.124 2.267 0.451
768W W 855 0.595 4.182 4.326
769W W 856 2.775 0.252 1.707
770W W 857 2.055 0.627 5.199
771W W 858 4.235 3.722 4.528
772W W 859 3.956 0.396 2.739
773W W 860 3.245 3.786 0.031
774W W 861 1.514 1.419 3.903
775W W 862 3.791 0.569 5.471
776W W 863 2.155 1.937 5.369
777W W 864 4.605 0.926 5.666
778W W 865 2.501 3.511 4.849
779W W 866 1.617 2.514 0.081
780W W 867 1.880 0.104 0.889
781W W 868 3.987 2.291 1.728
782W W 869 0.091 1.531 0.234
783W W 870 0.901 3.321 4.086
784W W 871 1.307 3.585 3.264
785W W 872 0.570 1.451 2.068
786W W 873 0.758 3.350 3.610
787W W 874 0.573 3.982 5.436
788W W 875 0.766 1.544 0.057
789W W 876 2.703 2.910 5.491
790W W 877 0.375 1.010 4.899
791W W 878 1.786 4.210 3.982
792W W 879 3.118 1.405 1.303
793W W 880 3.336 0.934 5.474
794W W 881 0.971 1.400 2.431
795W W 882 3.038 0.546 2.729
796W W 883 4.790 2.302 2.858
797W W 884 4.500 0.656 1.182
798W W 885 3.412 4.715 2.936
799W W 886 2.393 3.242 1.322
800W W 887 3.437 4.364 1.172
801W W 888 1.498 4.069 0.880
802W W 889 4.602 0.516 0.409
803W W 890 3.495 3.299 5.850
804W W 891 2.486 3.387 0.753
805W W 892 0.552 4.480 0.484
806W W 893 4.142 3.670 3.267
807W W 894 4.342 4.960 1.194
808W W 895 4.692 2.736 3.998
809W W 896 3.559 1.910 4.507
810W W 897 3.501 2.242 1.492
811W W 898 1.078 2.950 4.818
812W W 899 0.277 3.064 2.640
813W W 900 4.286 3.183 3.310
814W W 901 4.027 4.263 0.005
815W W 902 4.160 1.167 2.486
816W W 903 2.700 4.146 4.581
817W W 904 4.706 2.949 0.206
818W W 905 2.441 4.990 0.386
819W W 906 4.450 4.902 3.726
820W W 907 4.205 4.242 2.814
821W W 908 4.573 0.717 3.137
822W W 909 0.615 2.898 3.086
823W W 910 2.791 3.340 0.414
824W W 911 0.628 3.917 3.862
825W W 912 2.287 4.367 5.886
826W W 913 1.987 4.839 4.523
827W W 914 3.615 1.634 2.811
828W W 915 4.482 4.228 0.127
829W W 916 3.567 1.426 0.380
830W W 917 3.860 2.572 3.870
831W W 918 2.574 4.465 3.248
832W W 919 2.479 4.375 3.720
833W W 920 4.291 3.766 0.266
834W W 921 1.896 1.822 1.551
835W W 922 2.803 4.085 3.989
836W W 923 3.532 0.244 2.279
837W W 924 4.173 2.308 3.058
838W W 925 3.979 3.630 4.137
839W W 926 2.535 4.747 2.788
840W W 927 4.774 3.845 4.510
841W W 928 3.444 0.778 2.127
842W W 929 0.352 2.412 2.819
843W W 930 1.034 0.399 0.189
844W W 931 4.728 3.063 3.229
845W W 932 4.282 4.062 2.293
846W W 933 0.709 3.545 0.826
847W W 934 0.220 0.223 1.049
848W W 935 4.848 0.043 4.028
849W W 936 4.969 1.166 2.333
850W W 937 2.058 3.352 3.634
851W W 938 2.697 0.366 0.345
852W W 939 0.217 3.704 2.737
853W W 940 2.163 4.339 5.022
854W W 941 1.855 4.217 1.289
855W W 942 4.571 1.971 4.320
856W W 943 4.330 0.741 1.909
857W W 944 4.123 0.892 5.469
858W W 945 0.707 4.058 0.733
859W W 946 1.994 0.086 4.048
860W W 947 3.668 0.098 1.231
861W W 948 4.468 2.397 2.573
862W W 949 4.189 1.308 4.728
863W W 950 1.473 1.745 4.223
864W W 951 2.427 0.675 0.476
865W W 952 4.353 3.235 4.801
866W W 953 2.040 3.666 4.510
867W W 954 1.403 3.703 3.172
868W W 955 2.293 1.438 4.273
869W W 956 1.656 3.956 4.727
870W W 957 0.088 4.240 2.533
871W W 958 1.076 3.288 2.488
872W W 959 1.343 2.718 1.177
873W W 960 2.959 3.804 1.931
874W W 961 1.297 4.587 4.767
875W W 962 0.728 1.773 2.470
876W W 963 4.619 0.761 2.382
877W W 964 3.855 4.059 0.406
878W W 965 4.703 3.132 0.793
879W W 966 1.956 1.442 3.763
880W W 967 1.022 1.082 3.769
881W W 968 4.574 2.714 5.570
882W W 969 1.359 0.863 0.372
883W W 970 4.685 1.278 0.300
884W W 971 3.840 2.246 0.149
885W W 972 2.276 1.273 5.144
886W W 973 0.330 0.495 5.831
887W W 974 2.462 0.347 4.679
888W W 975 3.018 1.693 4.742
889W W 976 3.826 1.404 1.392
890W W 977 0.115 0.840 2.680
891W W 978 3.089 3.841 5.278
892W W 979 0.626 1.477 0.623
893W W 980 4.637 2.836 1.804
894W W 981 1.570 0.020 1.886
895W W 982 0.408 2.551 3.311
896W W 983 4.846 4.063 2.922
897W W 984 0.461 3.603 5.049
898W W 985 2.488 1.751 1.302
899W W 986 1.589 2.266 5.033
900W W 987 3.371 2.489 0.121
901W W 988 1.154 3.890 0.634
902W W 989 0.545 0.966 1.793
903W W 990 3.053 0.840 3.320
904W W 991 4.179 4.213 1.550
905W W 992 3.358 3.447 3.367
906W W 993 0.902 0.175 5.480
907W W 994 4.697 0.021 5.240
908W W 995 1.638 3.122 1.508
909W W 996 4.158 0.849 2.846
910W W 997 3.810 2.675 0.421
911W W 998 2.606 0.138 2.323
912W W 999 4.004 4.778 5.043
913W W 1000 2.529 1.595 5.486
914W W 1001 3.189 0.260 1.623
915W W 1002 2.642 0.860 2.369
916W W 1003 0.583 0.407 2.066
917W W 1004 2.027 0.982 4.960
918W W 1005 4.067 0.117 5.864
919W W 1006 1.932 0.087 5.334
920W W 1007 4.263 1.581 2.377
921W W 1008 2.848 4.116 5.620
922W W 1009 0.796 0.163 4.707
923W W 1010 0.910 1.776 5.500
924W W 1011 1.997 4.598 4.149
925W W 1012 0.283 2.899 5.420
926W W 1013 3.876 0.203 3.486
927W W 1014 2.356 2.239 5.827
928W W 1015 4.055 2.486 5.514
929W W 1016 2.850 0.935 4.297
930W W 1017 0.701 0.222 5.966
931W W 1018 1.129 1.125 3.029
932W W 1019 4.500 4.775 4.314
933W W 1020 3.933 4.942 1.607
934W W 1021 4.315 2.981 2.494
935W W 1022 3.876 0.243 1.925
936W W 1023 1.783 3.546 1.441
937W W 1024 3.135 1.371 3.961
938W W 1025 4.698 3.620 5.537
939W W 1026 2.681 4.847 1.588
940W W 1027 2.412 0.240 2.775
941W W 1028 2.621 3.976 0.723
942W W 1029 4.175 4.461 4.109
943W W 1030 1.673 3.882 1.885
944W W 1031 3.558 4.898 2.021
945W W 1032 2.586 2.576 4.654
946W W 1033 4.896 1.044 4.059
947W W 1034 4.125 1.365 5.255
948W W 1035 3.544 3.469 1.449
949W W 1036 4.246 1.688 0.565
950W W 1037 1.918 4.140 3.398
951W W 1038 4.742 3.861 2.434
952W W 1039 0.007 1.465 1.284
953W W 1040 3.970 1.590 0.103
954W W 1041 0.036 0.959 0.173
955W W 1042 2.411 2.676 1.078
956W W 1043 3.669 3.920 3.259
957W W 1044 3.422 1.732 3.716
958W W 1045 1.963 0.036 2.037
959W W 1046 4.999 3.491 2.185
960W W 1047 1.724 3.821 3.753
961W W 1048 1.629 3.062 4.454
962W W 1049 0.620 2.232 0.597
963W W 1050 1.189 3.356 3.033
964W W 1051 1.200 2.767 4.143
965W W 1052 0.191 1.539 4.041
966W W 1053 0.132 1.349 4.816
5.00000 5.00000 6.00000
Please Log in or Create an account to join the conversation.
- djurre
- Offline
- Admin
Less
More
- Posts: 272
11 years 3 months ago #1367
by djurre
Replied by djurre on topic simulation blow up in the protein in water simulation
The gro and top files look fine, so there is probably something wrong with your mdp options (or the Protein_A.itp). Did you change anything compare to the tutorial files?
You can't use Protein_A as a group, because it is not one of the groups grompp recognizes by default. Just 'Protein' should work.
You can't use Protein_A as a group, because it is not one of the groups grompp recognizes by default. Just 'Protein' should work.
Please Log in or Create an account to join the conversation.
- junfeng
- Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 13
11 years 3 months ago #1370
by junfeng
Replied by junfeng on topic simulation blow up in the protein in water simulation
Here are some of the observations:
1. If I do minimization too long(I know we do not have to, but it is a testcase), lets say 5000 steps, I can see water becomes scattered in the box and create vacumm space. Why? I am just curious to know.
2. I only get mdrun error when applying position restraint. I just put "define = -DPOSRES" as one line in the mdp file:
define = -DPOSRES
integrator = md
tinit = 0.0
dt = 0.02
nsteps = 5000
....
Error messages are:
Program mdrun, VERSION 4.5.5
Source code file: /tmp/build/gromacs-4.5.5/src/mdlib/domdec.c, line: 3266
Software inconsistency error:
Inconsistent DD boundary staggering limits!
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors
The Protein_A.itp file has those lines defining position restraints:
#ifdef POSRES
#ifndef POSRES_FC
#define POSRES_FC 1000.00
#endif
[ position_restraints ]
1 1 POSRES_FC POSRES_FC POSRES_FC
3 1 POSRES_FC POSRES_FC POSRES_FC
5 1 POSRES_FC POSRES_FC POSRES_FC
....
Anything I am doing wrong? When I remove the line, mdrun runs fine.
1. If I do minimization too long(I know we do not have to, but it is a testcase), lets say 5000 steps, I can see water becomes scattered in the box and create vacumm space. Why? I am just curious to know.
2. I only get mdrun error when applying position restraint. I just put "define = -DPOSRES" as one line in the mdp file:
define = -DPOSRES
integrator = md
tinit = 0.0
dt = 0.02
nsteps = 5000
....
Error messages are:
Program mdrun, VERSION 4.5.5
Source code file: /tmp/build/gromacs-4.5.5/src/mdlib/domdec.c, line: 3266
Software inconsistency error:
Inconsistent DD boundary staggering limits!
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors
The Protein_A.itp file has those lines defining position restraints:
#ifdef POSRES
#ifndef POSRES_FC
#define POSRES_FC 1000.00
#endif
[ position_restraints ]
1 1 POSRES_FC POSRES_FC POSRES_FC
3 1 POSRES_FC POSRES_FC POSRES_FC
5 1 POSRES_FC POSRES_FC POSRES_FC
....
Anything I am doing wrong? When I remove the line, mdrun runs fine.
Please Log in or Create an account to join the conversation.
Time to create page: 0.117 seconds