[gmx-users] PMF curve in umbrella sampling
Justin Lemkul
jalemkul at vt.edu
Sun Aug 31 15:01:39 CEST 2014
On 8/30/14, 8:09 AM, Mana Ib wrote:
> Thankyou for your response. I spaced them at approx 0.05nm because at the
> 473rd configuration my ligand becomes solvated...and completely dissociated
> from the protein and there is a jump in the COM distances. Would you
> recommend running windows for configurations beyond 473 to get an accurate
> PMF curve?
>
> COM distances:
>
> 0 1.2500689
> 1 1.2390118
> 2 1.2656376
> 3 1.2382807
> 4 1.2464908
> 5 1.2613748
> 6 1.2571518
> 7 1.2494564
> 8 1.2383828
> 9 1.2645215
> 10 1.2555224
> 11 1.2915937
> 12 1.2589550
> 13 1.2495953
> 14 1.2489617
> 15 1.2657266
> 16 1.2611536
> 17 1.2734816
> 18 1.2627461
> 19 1.2537713
> 20 1.2643420
> 21 1.2796929
> 22 1.2557689
> 23 1.2522986
> 24 1.2710813
> 25 1.2805812
> 26 1.2488314
> 27 1.2324920
> 28 1.2218119
> 29 1.2351364
> 30 1.2542222
> 31 1.2607237
> 32 1.2823184
> 33 1.2744044
> 34 1.2816412
> 35 1.2946619
> 36 1.2658573
> 37 1.2778631
> 38 1.2684767
> 39 1.2577963
> 40 1.2658514
> 41 1.2675236
> 42 1.2645024
> 43 1.2517917
> 44 1.2668618
> 45 1.2837279
> 46 1.2711920
> 47 1.2984477
> 48 1.2850081
> 49 1.2738078
> 50 1.2791895
> 51 1.2671049
> 52 1.2689266
> 53 1.2527233
> 54 1.2541883
> 55 1.2683328
> 56 1.2879772
> 57 1.2765738
> 58 1.2745949
> 59 1.2624943
> 60 1.2713360
> 61 1.2903701
> 62 1.2538780
> 63 1.2524761
> 64 1.2804133
> 65 1.2904843
> 66 1.2767571
> 67 1.2811158
> 68 1.2873763
> 69 1.2897247
> 70 1.2967854
> 71 1.2898058
> 72 1.2866045
> 73 1.2680842
> 74 1.2828430
> 75 1.2517999
> 76 1.2789755
> 77 1.2674298
> 78 1.2963352
> 79 1.2863842
> 80 1.2686276
> 81 1.2527305
> 82 1.2675610
> 83 1.2817050
> 84 1.2519698
> 85 1.2547150
> 86 1.2316085
> 87 1.2301512
> 88 1.2587688
> 89 1.2676184
> 90 1.2682347
> 91 1.2762364
> 92 1.2774154
> 93 1.2711686
> 94 1.2815300
> 95 1.3117696
> 96 1.3037083
> 97 1.2877588
> 98 1.3003120
> 99 1.2830641
> 100 1.2736199
> 101 1.2975351
> 102 1.2716285
> 103 1.2636745
> 104 1.2595536
> 105 1.2820042
> 106 1.2727789
> 107 1.2464533
> 108 1.2609475
> 109 1.2909839
> 110 1.2857704
> 111 1.2857469
> 112 1.2838980
> 113 1.2866713
> 114 1.2899315
> 115 1.2773947
> 116 1.2701035
> 117 1.2897719
> 118 1.2819400
> 119 1.3044168
> 120 1.2997466
> 121 1.2958813
> 122 1.2790420
> 123 1.2786862
> 124 1.2843164
> 125 1.3100673
> 126 1.2898589
> 127 1.2878088
> 128 1.2788408
> 129 1.2817291
> 130 1.2892330
> 131 1.2841049
> 132 1.2907283
> 133 1.2960732
> 134 1.2822367
> 135 1.3024569
> 136 1.2965143
> 137 1.2839130
> 138 1.2765539
> 139 1.2846087
> 140 1.2716116
> 141 1.2829932
> 142 1.2692751
> 143 1.3112148
> 144 1.3305217
> 145 1.3154910
> 146 1.2995077
> 147 1.2961320
> 148 1.3201323
> 149 1.3076353
> 150 1.3050537
> 151 1.3059070
> 152 1.3154420
> 153 1.2943887
> 154 1.3121384
> 155 1.3134962
> 156 1.3178825
> 157 1.3217572
> 158 1.2944893
> 159 1.2979667
> 160 1.2917393
> 161 1.2989479
> 162 1.3068420
> 163 1.3138773
> 164 1.2800533
> 165 1.2904462
> 166 1.2946355
> 167 1.2841026
> 168 1.2830913
> 169 1.2916815
> 170 1.3171769
> 171 1.2839959
> 172 1.2902473
> 173 1.3021219
> 174 1.3086892
> 175 1.3062795
> 176 1.2896782
> 177 1.2646221
> 178 1.2967244
> 179 1.3318710
> 180 1.3260037
> 181 1.3066446
> 182 1.3087828
> 183 1.3031635
> 184 1.2651044
> 185 1.3077284
> 186 1.2997077
> 187 1.2937896
> 188 1.3135617
> 189 1.3186882
> 190 1.3199843
> 191 1.3641998
> 192 1.3608552
> 193 1.3191408
> 194 1.3369676
> 195 1.3495121
> 196 1.3608030
> 197 1.3640209
> 198 1.3769726
> 199 1.3143706
> 200 1.3277380
> 201 1.3327760
> 202 1.3275329
> 203 1.3249296
> 204 1.3207476
> 205 1.3446074
> 206 1.3251934
> 207 1.3521178
> 208 1.3415477
> 209 1.3205338
> 210 1.3183049
> 211 1.3279040
> 212 1.3370273
> 213 1.3558873
> 214 1.3275462
> 215 1.3397077
> 216 1.3265324
> 217 1.3250760
> 218 1.3557339
> 219 1.3370665
> 220 1.3299704
> 221 1.3431152
> 222 1.3304195
> 223 1.3742563
> 224 1.3224043
> 225 1.3176907
> 226 1.3264394
> 227 1.3246692
> 228 1.3441764
> 229 1.3347285
> 230 1.3389533
> 231 1.3308688
> 232 1.3257663
> 233 1.3243916
> 234 1.3384953
> 235 1.3148066
> 236 1.2998172
> 237 1.3078777
> 238 1.3343482
> 239 1.3064271
> 240 1.3530262
> 241 1.3190423
> 242 1.3246952
> 243 1.3256948
> 244 1.3378791
> 245 1.3348513
> 246 1.3224670
> 247 1.3466573
> 248 1.3461218
> 249 1.3204277
> 250 1.3261340
> 251 1.3477811
> 252 1.3435458
> 253 1.3670396
> 254 1.3363574
> 255 1.3268965
> 256 1.3046312
> 257 1.3266972
> 258 1.3626263
> 259 1.3708274
> 260 1.3452878
> 261 1.3339913
> 262 1.3417501
> 263 1.3323883
> 264 1.3441674
> 265 1.3532716
> 266 1.3320799
> 267 1.3409791
> 268 1.3437917
> 269 1.3395978
> 270 1.3411486
> 271 1.3256128
> 272 1.3365294
> 273 1.3508692
> 274 1.3467736
> 275 1.3287274
> 276 1.3815287
> 277 1.3535491
> 278 1.3791600
> 279 1.3642347
> 280 1.3533387
> 281 1.3623170
> 282 1.3466438
> 283 1.3740207
> 284 1.3444097
> 285 1.3812722
> 286 1.3612189
> 287 1.3845141
> 288 1.3615390
> 289 1.3843898
> 290 1.3574173
> 291 1.3688576
> 292 1.3568767
> 293 1.3610542
> 294 1.3538148
> 295 1.3700429
> 296 1.3835357
> 297 1.3880055
> 298 1.3527056
> 299 1.3538814
> 300 1.3621348
> 301 1.3605335
> 302 1.3750969
> 303 1.3688582
> 304 1.3865705
> 305 1.3780358
> 306 1.3675889
> 307 1.3603872
> 308 1.3537391
> 309 1.3766954
> 310 1.3766360
> 311 1.3709415
> 312 1.3782817
> 313 1.3907872
> 314 1.3541425
> 315 1.3769609
> 316 1.3653841
> 317 1.3754011
> 318 1.3792280
> 319 1.3529605
> 320 1.3837168
> 321 1.3651855
> 322 1.3889990
> 323 1.3743008
> 324 1.3773041
> 325 1.3651620
> 326 1.3719771
> 327 1.3560431
> 328 1.3871281
> 329 1.3648498
> 330 1.3811992
> 331 1.3798934
> 332 1.3832864
> 333 1.3879728
> 334 1.3658290
> 335 1.3798630
> 336 1.3452870
> 337 1.3741655
> 338 1.3806974
> 339 1.3609663
> 340 1.4018263
> 341 1.3735665
> 342 1.3735117
> 343 1.3783028
> 344 1.3821008
> 345 1.3655910
> 346 1.3664550
> 347 1.3615848
> 348 1.3874092
> 349 1.3827159
> 350 1.3833929
> 351 1.3965851
> 352 1.4005339
> 353 1.3731993
> 354 1.3933755
> 355 1.4099180
> 356 1.3948082
> 357 1.3856125
> 358 1.3767538
> 359 1.3927557
> 360 1.3798248
> 361 1.3849571
> 362 1.3850863
> 363 1.3809032
> 364 1.3837097
> 365 1.3981184
> 366 1.3897134
> 367 1.3719181
> 368 1.3668927
> 369 1.3755823
> 370 1.3978622
> 371 1.4025136
> 372 1.3865751
> 373 1.3865086
> 374 1.4005067
> 375 1.3892016
> 376 1.4685237
> 377 1.6416547
> 378 1.7369542
> 379 1.7453635
> 380 1.7462621
> 381 1.7428764
> 382 1.7567976
> 383 1.7493412
> 384 1.7496111
> 385 1.7471077
> 386 1.7242872
> 387 1.7373158
> 388 1.7245857
> 389 1.7423515
> 390 1.7726310
> 391 1.7427715
> 392 1.7554132
> 393 1.7550788
> 394 1.7818098
> 395 1.7333920
> 396 1.7768469
> 397 1.7746025
> 398 1.7427593
> 399 1.7602735
> 400 1.7586886
> 401 1.7801439
> 402 1.7416029
> 403 1.7504994
> 404 1.7656693
> 405 1.7537409
> 406 1.7633922
> 407 1.7597046
> 408 1.7520651
> 409 1.7435281
> 410 1.7482374
> 411 1.7536854
> 412 1.7445352
> 413 1.7690600
> 414 1.7426364
> 415 1.7697076
> 416 1.7535267
> 417 1.7374755
> 418 1.7249068
> 419 1.7559983
> 420 1.7714272
> 421 1.7489988
> 422 1.7789098
> 423 1.7556661
> 424 1.7498537
> 425 1.7209381
> 426 1.7868423
> 427 1.7552314
> 428 1.7615218
> 429 1.7581145
> 430 1.7319311
> 431 1.7728666
> 432 1.7533555
> 433 1.7472804
> 434 1.7643290
> 435 1.7744331
> 436 1.7526252
> 437 1.7709931
> 438 1.7331252
> 439 1.7507143
> 440 1.7979895
> 441 1.7770579
> 442 1.7759854
> 443 1.8038515
> 444 1.7722791
> 445 1.7890617
> 446 1.7675257
> 447 1.7821010
> 448 1.7638472
> 449 1.7543905
> 450 1.7507652
> 451 1.7842894
> 452 1.7834905
> 453 1.7813838
> 454 1.7773324
> 455 1.7524773
> 456 1.7914710
> 457 1.7911654
> 458 1.7771055
> 459 1.7913604
> 460 1.7621474
> 461 1.7815893
> 462 1.7682685
> 463 1.7389239
> 464 1.7635071
> 465 1.7635591
> 466 1.8023010
> 467 1.7451056
> 468 1.8103623
> 469 1.7851202
> 470 1.7912778
> 471 1.8105056
> 472 1.8074669
> 473 1.8579408
> 474 2.1607230
> 475 3.5636280
> 476 4.6066022
> 477 5.1597238
> 478 5.3922682
> 479 5.4833398
> 480 5.5982175
> 481 5.6742902
> 482 5.6503868
> 483 5.7863832
> 484 5.8687239
> 485 5.8829122
> 486 5.8874602
> 487 5.9502139
> 488 5.9497595
> 489 5.9120698
> 490 5.9541750
> 491 5.8905106
> 492 5.8934441
> 493 5.9666514
> 494 6.0210390
> 495 6.0501065
> 496 5.9903316
> 497 6.0493150
> 498 6.0622525
> 499 6.0904546
> 500 6.0461636
>
Your spacing is inadequate for defining a good reaction coordinate. Either your
pull rate or force constant needs to be adjusted. You have minimal separation,
followed by sudden changes in the distance.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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