[gmx-users] umbrella-histogram-windows
Justin A. Lemkul
jalemkul at vt.edu
Mon Feb 6 15:10:56 CET 2012
parto haghighi wrote:
> Dear gmx users
> I am working on an umbrella sampling system.(lipid bilayer+drug).
> I have used distance
> I have used lipid as a refrence group and drug as a pull group.in
> npt_umbrella mdp I have used constraint for refrence group and in
> md_umbrella I have removed the constraint.
I'm not clear on what you're doing here. An .mdp file would be extremely helpful.
> After that my summery.dat file contains following data:
> 0 2.2163574
> 1 2.2125353
> 2 2.1688467
> 3 2.1041310
> 4 2.0907198
> 5 2.0372755
> 6 2.0344109
> 7 2.0205807
> 8 2.0188276
> 9 2.0063477
> 10 2.0100271
> 11 1.9960003
> 12 2.0011811
> 13 1.9741284
> 14 1.9680872
> 15 1.9487932
> 16 1.8766397
> 17 1.7200924
> 18 1.6762846
> 19 1.5760427
> 20 1.4725303
> 21 1.4852792
> 22 1.3151125
> 23 1.1968731
> 24 1.1196491
> 25 1.0879384
> 26 1.1214086
> 27 1.0457795
> 28 1.1297384
> 29 1.0547690
> 30 1.1172924
> 31 1.2132208
> 32 1.2790826
> 33 1.2556396
> 34 1.2034254
> 35 1.0906192
> 36 1.0417964
> 37 1.1047103
> 38 1.1989108
> 39 1.2073846
> 40 1.1673214
> 41 1.0815340
> 42 1.1169575
> 43 1.1769875
> 44 1.2455147
> 45 1.1928731
> 46 1.1054069
> 47 1.0790326
> 48 1.1362654
> 49 1.1214680
> 50 1.0738213
> 51 1.0363408
> 52 1.0989448
> 53 1.1428183
> 54 1.1201882
> 55 1.1889806
> 56 1.2362384
> 57 1.2051160
> 58 1.2037644
> 59 1.2171633
> 60 1.2363109
> 61 1.2392871
> 62 1.2603214
> 63 1.2539344
> 64 1.1282977
> 65 1.1482411
> 66 1.1867742
> 67 1.1649172
> 68 1.1241708
> 69 1.1105422
> 70 1.1251793
> 71 1.0987285
> 72 1.1251851
> 73 1.1679051
> 74 1.1052191
> 75 1.1244428
> 76 1.1386129
> 77 1.1365076
> 78 1.1383851
> 79 1.1449340
> 80 1.1346834
> 81 1.1167825
> 82 1.0945875
> 83 1.1300997
> 84 1.1428297
> 85 1.1867594
> 86 1.1590696
> 87 1.1404225
> 88 1.1742213
> 89 1.1349461
> 90 1.1314867
> 91 1.1361587
> 92 1.1224793
> 93 1.1788386
> 94 1.1498441
> 95 1.1506270
> 96 1.1064949
> 97 1.1546595
> 98 1.1564190
> 99 1.0714226
> 100 1.1199773
> 101 1.1281228
> 102 1.1524893
> 103 1.1595686
> 104 1.1536553
> 105 1.1890795
> 106 1.1438330
> 107 1.1567581
> 108 1.1610076
> 109 1.1843101
> 110 1.1461171
> 111 1.1774145
> 112 1.1266857
> 113 1.1730814
> 114 1.1112221
> 115 1.1658539
> 116 1.1526571
> 117 1.1057193
> 118 1.1287234
> 119 1.2012605
> 120 1.1389650
> 121 1.1590703
> 122 1.1685155
> 123 1.1321938
> 124 1.1486048
> 125 1.1461945
> 126 1.1769872
> 127 1.1249954
> 128 1.1714567
> 129 1.1397712
> 130 1.2048318
> 131 1.1261573
> 132 1.1649654
> 133 1.1346296
> 134 1.1994447
> 135 1.1558460
> 136 1.1871395
> 137 1.1626594
> 138 1.1184026
> 139 1.1341229
> 140 1.1324711
> 141 1.1030517
> 142 1.1764932
> 143 1.1264903
> 144 1.1322395
> 145 1.1227130
> 146 1.1129291
> 147 1.1315118
> 148 1.1746687
> 149 1.1266127
> 150 1.1803793
> 151 1.1231681
> 152 1.1136831
> 153 1.1268005
> 154 1.1447661
> 155 1.1451746
> 156 1.1446071
> 157 1.1281052
> 158 1.1278596
> 159 1.1505933
> 160 1.1632346
> 161 1.1634330
> 162 1.1200876
> 163 1.1263421
> 164 1.1532616
> 165 1.1385699
> 166 1.1633223
> 167 1.1415736
> 168 1.1360134
> 169 1.1299793
> 170 1.1757061
> 171 1.1165316
> 172 1.1547863
> 173 1.1442331
> 174 1.1547793
> 175 1.1619559
> 176 1.0891477
> 177 1.2072016
> 178 1.0957750
> 179 1.1775378
> 180 1.1678475
> 181 1.1312756
> 182 1.1353923
> 183 1.1531162
> 184 1.1581031
> 185 1.1339137
> 186 1.1845239
> 187 1.1742307
> 188 1.1601242
> 189 1.1375409
> 190 1.1153691
> 191 1.1614760
> 192 1.1293349
> 193 1.2212412
> 194 1.1004681
> 195 1.1768598
> 196 1.1651047
> 197 1.1433749
> 198 1.1317539
> 199 1.1521342
> 200 1.1553539
> 201 1.1589068
> 202 1.1888202
> 203 1.1139559
> 204 1.0850017
> 205 1.1767445
> 206 1.1000916
> 207 1.1339216
> 208 1.1156967
> 209 1.1692301
> 210 1.1610108
> 211 1.1196257
> 212 1.0764190
> 213 1.1954692
> 214 1.1750859
> 215 1.1475511
> 216 1.2494902
> 217 1.3200271
> 218 1.3524807
> 219 1.2711932
> 220 1.2862429
> 221 1.2441974
> 222 1.1245995
> 223 1.1403349
> 224 1.1821948
> 225 1.1194941
> 226 1.2166983
> 227 1.1187817
> 228 1.1529719
> 229 1.1997244
> 230 1.2553700
> 231 1.2353689
> 232 1.2522210
> 233 1.2437250
> 234 1.2698068
> 235 1.2502098
> 236 1.2633507
> 237 1.2545269
> 238 1.1212504
> 239 1.2201137
> 240 1.1697107
> 241 1.1291697
> 242 1.1705309
> 243 1.1632101
> 244 1.1949524
> 245 1.0947707
> 246 1.1494623
> 247 1.1255785
> 248 1.1695995
> 249 1.1463469
> 250 1.1618913
> 251 1.1328190
> 252 1.1561620
> 253 1.1524103
> 254 1.1164197
> 255 1.2098684
> 256 1.0705856
> 257 1.1655772
> 258 1.1455529
> 259 1.1588525
> 260 1.1378038
> 261 1.2334902
> 262 1.1669033
> 263 1.1166701
> 264 1.2513789
> 265 1.2197116
> 266 1.1542124
> 267 1.1439006
> 268 1.1764008
> 269 1.1560290
> 270 1.1297302
> 271 1.1459278
> 272 1.1193644
> 273 1.1963632
> 274 1.1195823
> 275 1.1798624
> 276 1.1239418
> 277 1.1408878
> 278 1.1209821
> 279 1.1570644
> 280 1.1687217
> 281 1.1703171
> 282 1.1599334
> 283 1.2152494
> 284 1.1819685
> 285 1.1444129
> 286 1.1373526
> 287 1.1522148
> 288 1.1955314
> 289 1.1804147
> 290 1.1278866
> 291 1.1855028
> 292 1.1350925
> 293 1.1918853
> 294 1.3350349
> 295 1.3654863
> 296 1.3674002
> 297 1.2899203
> 298 1.2829879
> 299 1.3052024
> 300 1.3288844
> 301 1.2837309
> 302 1.3256962
> 303 1.3243275
> 304 1.2473432
> 305 1.2359587
> 306 1.2649387
> 307 1.2660151
> 308 1.1724662
> 309 1.0874159
> 310 1.1483515
> 311 1.1234104
> 312 1.0911723
> 313 1.1726278
> 314 1.1236658
> 315 1.1503312
> 316 1.1483864
> 317 1.1385110
> 318 1.1450268
> 319 1.1258433
> 320 1.1607553
> 321 1.1851472
> 322 1.0866253
> 323 1.1584546
> 324 1.1706716
> 325 1.1875124
> 326 1.1405223
> 327 1.1409515
> 328 1.1348391
> 329 1.1583944
> 330 1.1505178
> 331 1.1372125
> 332 1.1527471
> 333 1.1294298
> 334 1.1278995
> 335 1.1661187
> 336 1.1231481
> 337 1.1155541
> 338 1.1182202
> 339 1.2047386
> 340 1.3277398
> 341 1.3305781
> 342 1.3356986
> 343 1.3074728
> 344 1.3149188
> 345 1.3659440
> 346 1.2956467
> 347 1.2984017
> 348 1.3240537
> 349 1.3195872
> 350 1.1910413
> 351 1.1419021
> 352 1.2791880
> 353 1.2110095
> 354 1.2410124
> 355 1.2374715
> 356 1.2517792
> 357 1.2964147
> 358 1.2125144
> 359 1.2226928
> 360 1.2527926
> 361 1.2526986
> 362 1.2585649
> 363 1.2118053
> 364 1.1915550
> 365 1.0578706
> 366 1.1585858
> 367 1.2330620
> 368 1.2205206
> 369 1.2902780
> 370 1.2496578
> 371 1.3022352
> 372 1.2931545
> 373 1.3098337
> 374 1.2268461
> 375 1.2309457
> 376 1.1559575
> 377 1.1523703
> 378 1.2773541
> 379 1.2432717
> 380 1.2776868
> 381 1.2967623
> 382 1.3015278
> 383 1.2940338
> 384 1.2748120
> 385 1.2233861
> 386 1.2562447
> 387 1.2719577
> 388 1.3442591
> 389 1.2361699
> 390 1.2806933
> 391 1.2778905
> 392 1.3138871
> 393 1.3569471
> 394 1.2524719
> 395 1.2874336
> 396 1.2607288
> 397 1.2356847
> 398 1.3131601
> 399 1.2253601
> 400 1.1105402
> 401 1.1580552
> 402 1.1277891
> 403 1.1714592
> 404 1.0912436
> 405 1.1864986
> 406 1.1878401
> 407 1.1372809
> 408 1.1702988
> 409 1.2193290
> 410 1.2647056
> 411 1.2543653
> 412 1.3284186
> 413 1.3181866
> 414 1.3686719
> 415 1.4521370
> 416 1.4641754
> 417 1.4523519
> 418 1.5920088
> 419 1.5980577
> 420 1.5489434
> 421 1.4902735
> 422 1.5826549
> 423 1.5600006
> 424 1.5902211
> 425 1.5323428
> 426 1.5456631
> 427 1.5273204
> 428 1.5900084
> 429 1.5412893
> 430 1.5962194
> 431 1.5370157
> 432 1.4973781
> 433 1.5288886
> 434 1.5560608
> 435 1.5629433
> 436 1.5456027
> 437 1.5347616
> 438 1.5467555
> 439 1.5660588
> 440 1.5592589
> 441 1.5447172
> 442 1.5793159
> 443 1.5243505
> 444 1.5337485
> 445 1.5812923
> 446 1.5076854
> 447 1.5527291
> 448 1.5599996
> 449 1.5375631
> 450 1.5507294
> 451 1.4763156
> 452 1.5596538
> 453 1.4723976
> 454 1.4742548
> 455 1.4885223
> 456 1.5286931
> 457 1.5812750
> 458 1.5992634
> 459 1.6721720
> 460 1.5979157
> 461 1.5882409
> 462 1.6096119
> 463 1.6853847
> 464 1.5547028
> 465 1.4746356
> 466 1.5158916
> 467 1.4675600
> 468 1.5343397
> 469 1.3681053
> 470 1.5010762
> 471 1.4803838
> 472 1.4953094
> 473 1.5424787
> 474 1.5200848
> 475 1.5052415
> 476 1.4971479
> 477 1.6006268
> 478 1.5689414
> 479 1.5624480
> 480 1.5368186
> 481 1.5469188
> 482 1.5405121
> 483 1.5489655
> 484 1.5677957
> 485 1.5555471
> 486 1.5745570
> 487 1.5241419
> 488 1.5673757
> 489 1.5205972
> 490 1.5468128
> 491 1.5371502
> 492 1.5486749
> 493 1.5264599
> 494 1.5077617
> 495 1.6062210
> 496 1.5399962
> 497 1.5931936
> 498 1.6058899
> 499 1.6357416
> 500 1.5546903
>
> I have applied 0,3,9,15,16,17,18,19,20,22,39,42 and 51 (from 0 to
> 500) points for my umbrella sampling.following are my questions:
> 1.why do not the points descend regularly when the drug is going to
> center of membrane?
If you're measuring the total COM distance, there are x, y, and z components.
Depending on how you're doing the pulling (again, an .mdp file is essential
here), it may just be that your molecule is drifting in x and y, while there is
a steady decrease in z.
> 2.In my histogram curve I only have 1 peak on the 2nd point of my 13
> points above,why?
Either you didn't run umbrella sampling correctly, or you didn't plot the output
correctly. We can't tell.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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