[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

==================================================


More information about the gromacs.org_gmx-users mailing list