[gmx-users] PMF curve in umbrella sampling
Mana Ib
fullmeasure29 at gmail.com
Sat Aug 30 14:09:22 CEST 2014
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
On Fri, Aug 29, 2014 at 11:52 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 8/29/14, 2:08 PM, Mana Ib wrote:
>
>> Dear Users,
>>
>> I am doing an umbrella sampling for a protein-ligand complex, wherein I
>> first did an SMD run for 500 ps and generated 500 configurations, the COM
>> distances for these configurations start at 1.25nm for conf0 and so on
>> till
>> 6.4nm for conf500. Hence I used a 0.05nm spacing to select configurations
>> for the umbrella sampling windows.
>> I have currently completed running 2 windows, each window was subjected to
>> a 5ns mdrun.
>>
>> This is my mdp file parameters
>>
>> title = Umbrella pulling simulation
>> define = -DPOSRES
>> ; Run parameters
>> integrator = md
>> dt = 0.002
>> tinit = 0
>> nsteps = 2500000 ; 5 ns
>> nstcomm = 10
>> ; Output parameters
>> nstxout = 50000 ; every 100 ps
>> nstvout = 50000
>> nstfout = 5000
>> nstxtcout = 5000 ; every 10 ps
>> nstenergy = 5000
>> ; Bond parameters
>> constraint_algorithm = lincs
>> constraints = all-bonds
>> continuation = yes
>> ; Single-range cutoff scheme
>> nstlist = 5
>> ns_type = grid
>> rlist = 1.4
>> rcoulomb = 1.4
>> rvdw = 1.4
>> ; PME electrostatics parameters
>> coulombtype = PME
>> fourierspacing = 0.12
>> fourier_nx = 0
>> fourier_ny = 0
>> fourier_nz = 0
>> pme_order = 4
>> ewald_rtol = 1e-5
>> optimize_fft = yes
>> ; Berendsen temperature coupling is on in two groups
>> Tcoupl = Nose-Hoover
>> tc_grps = Protein Non-Protein
>> tau_t = 0.5 0.5
>> ref_t = 310 310
>> ; Pressure coupling is on
>> Pcoupl = Parrinello-Rahman
>> pcoupltype = isotropic
>> tau_p = 1.0
>> compressibility = 4.5e-5
>> ref_p = 1.0
>> refcoord_scaling = com
>> ; Generate velocities is off
>> gen_vel = no
>> ; Periodic boundary conditions are on in all directions
>> pbc = xyz
>> ; Long-range dispersion correction
>> DispCorr = EnerPres
>> ; Pull code
>> pull = umbrella
>> pull_geometry = distance
>> pull_dim = Y N N
>> pull_start = yes
>> pull_ngroups = 1
>> pull_group0 = Chain_A
>> pull_group1 = NL
>> pull_init1 = 0
>> pull_rate1 = 0.0
>> pull_k1 = 500 ; kJ mol^-1 nm^-2
>> pull_nstxout = 1000 ; every 2 ps
>> pull_nstfout = 1000 ; every 2 ps
>>
>>
>> When I use g_wham to plot the histogram and PMF curve for these 2 windows,
>> my plots don't seem to follow the general trend as given in
>> tutorials..(figure links below). Is this discrepancy because I have used
>> only files from 2 windows to plot these? Or are these due to some other
>> errors in the protocol?
>>
>> http://i46.photobucket.com/albums/f121/fullmeasure29/
>> histo_2win_zpsff19fe60.png
>>
>> http://i46.photobucket.com/albums/f121/fullmeasure29/pmf_
>> 2win_zps04adb8f7.png
>>
>>
> The two windows yield effectively overlapping distributions and a
> meaningless PMF. Space the windows further (0.05 nm is very tight) and run
> more windows for a real PMF as a function of a meaningful reaction
> coordinate.
>
> -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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