Re: metadynamics and pmf file

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Jul 05 2016 - 16:29:10 CDT

Hello Stefano, it does not make sense to let the boundaries for the angle
be expanded automatically from their values of 0:180. This is the reason
why the flag "expandBoundaries" is per-colvar.

Moreover, you defined the range to be -180:180 for an angle between three
bodies, for which the range is only 0:180. This is also stated in the
documentation:
http://www.ks.uiuc.edu/Research/namd/2.11/ug/node57.html#SECTION000134180000000000000

Nevertheless, the bias is only meaningless outside the 0:180 for the angle,
so your problem is only a visualization one.

Giacomo

On Mon, Jul 4, 2016 at 8:43 PM, Stefano Guglielmo <
stefano.guglielmo_at_unito.it> wrote:

> Dear all,
>
> I performed a metadynamics simulation biasing two variables: a distance
> and an angle; below is the colvar file I used:
>
> colvarsTrajFrequency 100 # output values every 100 steps
>
> colvar {
> name DistGloopGlu12
> upperboundary 50
> upperWall 30
> upperWallConstant 800
>
> distance {
> group1 {
> atomNumbersRange 5029-5073
> }
> group2 {
> atomNumbersRange 187-201
> }
> }
> }
>
>
> colvar {
> name DistLeu83
> lowerBoundary 2
> upperBoundary 50
> expandBoundaries on
> width 2
> distance {
> group1 {
> atomNumbers 5048
> }
> group2 {
> atomNumbers 1373
> }
> }
> }
> colvar {
> name angle
> lowerBoundary -180.0
> upperBoundary 180.0
> expandBoundaries on
> width 24
> angle {
> group1 {
> atomNumbers 1373
> }
> group2 {
> atomNumbers 5048
> }
> group3 {
> atomNumbers 5031
> }
> }
> }
> metadynamics {
> colvars DistLeu83 angle
> hillWeight 0.6
> newHillFrequency 1000
> wellTempered on
> biasTemperature 890
> hillWidth 1.25
> writeFreeEnergyFile on
> rebinGrids on
> }
>
> There is a discrepancy between the colvars trajectory (not attached) where
> the angle spans over 0-180 deg. and the pmf file here reported:
>
> # 2
> # -6 2 32 0
> # -180 24 19 0
>
> -5 -168 17.3738
> -5 -144 17.3738
> -5 -120 17.3738
> -5 -96 17.3738
> -5 -72 17.3738
> -5 -48 17.3738
> -5 -24 17.3738
> -5 0 17.3738
> -5 24 17.3738
> -5 48 17.3738
> -5 72 17.3738
> -5 96 17.3738
> -5 120 17.3738
> -5 144 17.3738
> -5 168 17.3738
> -5 192 17.3738
> -5 216 17.3738
> -5 240 17.3738
> -5 264 17.3738
>
> -3 -168 17.3738
> -3 -144 17.3738
> -3 -120 17.3738
> -3 -96 17.3738
> -3 -72 17.3738
> -3 -48 17.3738
> -3 -24 17.3738
> -3 0 17.3738
> -3 24 17.3738
> -3 48 17.3738
> -3 72 17.3738
> -3 96 17.3738
> -3 120 17.3738
> -3 144 17.3738
> -3 168 17.3738
> -3 192 17.3738
> -3 216 17.3738
> -3 240 17.3738
> -3 264 17.3738
>
> -1 -168 17.3738
> -1 -144 17.3738
> -1 -120 17.3738
> -1 -96 17.3738
> -1 -72 17.3738
> -1 -48 17.3738
> -1 -24 17.3738
> -1 0 17.3738
> -1 24 17.3735
> -1 48 17.3721
> -1 72 17.3665
> -1 96 17.3496
> -1 120 17.3487
> -1 144 17.3638
> -1 168 17.3721
> -1 192 17.3738
> -1 216 17.3738
> -1 240 17.3738
> -1 264 17.3738
>
> 1 -168 17.3738
> 1 -144 17.3738
> 1 -120 17.3738
> 1 -96 17.3738
> 1 -72 17.3738
> 1 -48 17.3738
> 1 -24 17.3736
> 1 0 17.3643
> 1 24 17.29
> 1 48 17.1011
> 1 72 16.6219
> 1 96 15.7034
> 1 120 15.8729
> 1 144 16.6647
> 1 168 17.2098
> 1 192 17.3653
> 1 216 17.3737
> 1 240 17.3738
> 1 264 17.3738
>
> 3 -168 17.3738
> 3 -144 17.3738
> 3 -120 17.3738
> 3 -96 17.3738
> 3 -72 17.3738
> 3 -48 17.3738
> 3 -24 17.3622
> 3 0 16.9916
> 3 24 14.9065
> 3 48 12.1873
> 3 72 8.86921
> 3 96 5.49378
> 3 120 8.34851
> 3 144 11.4278
> 3 168 15.0201
> 3 192 17.0493
> 3 216 17.3645
> 3 240 17.3738
> 3 264 17.3738
>
> 5 -168 17.3738
> 5 -144 17.3738
> 5 -120 17.3738
> 5 -96 17.3738
> 5 -72 17.3738
> 5 -48 17.3723
> 5 -24 17.1985
> 5 0 14.667
> 5 24 7.32882
> 5 48 1.40111
> 5 72 0.258836
> 5 96 2.35839
> 5 120 5.2525
> 5 144 3.92342
> 5 168 7.49857
> 5 192 15.017
> 5 216 17.2937
> 5 240 17.3736
> 5 264 17.3738
>
> 7 -168 17.3738
> 7 -144 17.3738
> 7 -120 17.3738
> 7 -96 17.3738
> 7 -72 17.3738
> 7 -48 17.3632
> 7 -24 16.4284
> 7 0 8.57087
> 7 24 1.70637
> 7 48 1.07733
> 7 72 3.18008
> 7 96 4.94548
> 7 120 5.83503
> 7 144 4.22616
> 7 168 5.635
> 7 192 13.7577
> 7 216 17.2325
> 7 240 17.3733
> 7 264 17.3738
>
> 9 -168 17.3738
> 9 -144 17.3738
> 9 -120 17.3738
> 9 -96 17.3738
> 9 -72 17.3738
> 9 -48 17.357
> 9 -24 15.965
> 9 0 5.78781
> 9 24 1.02722
> 9 48 3.55374
> 9 72 7.65012
> 9 96 7.36178
> 9 120 6.2057
> 9 144 3.96495
> 9 168 5.33444
> 9 192 13.7595
> 9 216 17.2296
> 9 240 17.3733
> 9 264 17.3738
>
> 11 -168 17.3738
> 11 -144 17.3738
> 11 -120 17.3738
> 11 -96 17.3738
> 11 -72 17.3738
> 11 -48 17.3585
> 11 -24 16.0869
> 11 0 7.19742
> 11 24 4.20908
> 11 48 5.14506
> 11 72 6.22961
> 11 96 5.58697
> 11 120 5.7486
> 11 144 5.5167
> 11 168 6.57286
> 11 192 14.1455
> 11 216 17.2467
> 11 240 17.3734
> 11 264 17.3738
>
> 13 -168 17.3738
> 13 -144 17.3738
> 13 -120 17.3738
> 13 -96 17.3738
> 13 -72 17.3738
> 13 -48 17.3595
> 13 -24 16.2724
> 13 0 9.42296
> 13 24 6.30961
> 13 48 5.05197
> 13 72 3.9567
> 13 96 4.9615
> 13 120 5.93754
> 13 144 5.4431
> 13 168 5.95895
> 13 192 14.0211
> 13 216 17.2459
> 13 240 17.3734
> 13 264 17.3738
>
> 15 -168 17.3738
> 15 -144 17.3738
> 15 -120 17.3738
> 15 -96 17.3738
> 15 -72 17.3738
> 15 -48 17.354
> 15 -24 15.9113
> 15 0 7.13332
> 15 24 2.99759
> 15 48 2.93278
> 15 72 3.36082
> 15 96 4.58005
> 15 120 3.65033
> 15 144 5.39848
> 15 168 6.36307
> 15 192 14.2793
> 15 216 17.2662
> 15 240 17.3735
> 15 264 17.3738
>
> 17 -168 17.3738
> 17 -144 17.3738
> 17 -120 17.3738
> 17 -96 17.3738
> 17 -72 17.3738
> 17 -48 17.3554
> 17 -24 15.954
> 17 0 6.58254
> 17 24 1.51286
> 17 48 3.63322
> 17 72 4.53236
> 17 96 4.6477
> 17 120 5.03664
> 17 144 6.31837
> 17 168 6.1763
> 17 192 14.0226
> 17 216 17.2565
> 17 240 17.3735
> 17 264 17.3738
>
> 19 -168 17.3738
> 19 -144 17.3738
> 19 -120 17.3738
> 19 -96 17.3738
> 19 -72 17.3738
> 19 -48 17.3533
> 19 -24 15.781
> 19 0 4.98371
> 19 24 0.797346
> 19 48 4.28258
> 19 72 4.4064
> 19 96 4.00258
> 19 120 4.43665
> 19 144 5.62044
> 19 168 5.1872
> 19 192 13.5779
> 19 216 17.2361
> 19 240 17.3734
> 19 264 17.3738
>
> 21 -168 17.3738
> 21 -144 17.3738
> 21 -120 17.3738
> 21 -96 17.3738
> 21 -72 17.3738
> 21 -48 17.3518
> 21 -24 15.702
> 21 0 5.31629
> 21 24 2.83055
> 21 48 3.59195
> 21 72 4.28659
> 21 96 3.59195
> 21 120 4.73137
> 21 144 6.02774
> 21 168 5.64349
> 21 192 13.5747
> 21 216 17.2294
> 21 240 17.3734
> 21 264 17.3738
>
> 23 -168 17.3738
> 23 -144 17.3738
> 23 -120 17.3738
> 23 -96 17.3738
> 23 -72 17.3738
> 23 -48 17.3547
> 23 -24 15.96
> 23 0 7.31569
> 23 24 4.58456
> 23 48 5.02747
> 23 72 4.75963
> 23 96 4.70032
> 23 120 5.44864
> 23 144 5.37482
> 23 168 4.63261
> 23 192 13.2579
> 23 216 17.2155
> 23 240 17.3733
> 23 264 17.3738
>
> 25 -168 17.3738
> 25 -144 17.3738
> 25 -120 17.3738
> 25 -96 17.3738
> 25 -72 17.3738
> 25 -48 17.3596
> 25 -24 16.2687
> 25 0 8.95861
> 25 24 5.7871
> 25 48 5.16011
> 25 72 4.68099
> 25 96 4.63222
> 25 120 3.71272
> 25 144 4.02979
> 25 168 4.30081
> 25 192 13.0441
> 25 216 17.2039
> 25 240 17.3732
> 25 264 17.3738
>
> 27 -168 17.3738
> 27 -144 17.3738
> 27 -120 17.3738
> 27 -96 17.3738
> 27 -72 17.3738
> 27 -48 17.3616
> 27 -24 16.3652
> 27 0 9.2675
> 27 24 5.66783
> 27 48 5.56324
> 27 72 4.8288
> 27 96 3.41329
> 27 120 3.07198
> 27 144 3.61407
> 27 168 3.63967
> 27 192 12.9504
> 27 216 17.2054
> 27 240 17.3733
> 27 264 17.3738
>
> 29 -168 17.3738
> 29 -144 17.3738
> 29 -120 17.3738
> 29 -96 17.3738
> 29 -72 17.3738
> 29 -48 17.3605
> 29 -24 16.3247
> 29 0 9.26993
> 29 24 5.67616
> 29 48 5.18268
> 29 72 3.58297
> 29 96 2.24729
> 29 120 2.51952
> 29 144 3.68291
> 29 168 4.0964
> 29 192 13.3022
> 29 216 17.2252
> 29 240 17.3734
> 29 264 17.3738
>
> 31 -168 17.3738
> 31 -144 17.3738
> 31 -120 17.3738
> 31 -96 17.3738
> 31 -72 17.3738
> 31 -48 17.3581
> 31 -24 16.2095
> 31 0 8.83103
> 31 24 5.23094
> 31 48 4.18443
> 31 72 1.08926
> 31 96 -0
> 31 120 3.07951
> 31 144 4.5002
> 31 168 3.91605
> 31 192 13.0899
> 31 216 17.2137
> 31 240 17.3733
> 31 264 17.3738
>
> 33 -168 17.3738
> 33 -144 17.3738
> 33 -120 17.3738
> 33 -96 17.3738
> 33 -72 17.3738
> 33 -48 17.3529
> 33 -24 15.8914
> 33 0 7.111
> 33 24 3.88056
> 33 48 2.46202
> 33 72 0.312859
> 33 96 0.848916
> 33 120 3.10579
> 33 144 3.88904
> 33 168 3.87688
> 33 192 12.8491
> 33 216 17.1858
> 33 240 17.3731
> 33 264 17.3738
>
> 35 -168 17.3738
> 35 -144 17.3738
> 35 -120 17.3738
> 35 -96 17.3738
> 35 -72 17.3738
> 35 -48 17.3485
> 35 -24 15.5719
> 35 0 5.00225
> 35 24 2.30686
> 35 48 2.62096
> 35 72 2.19787
> 35 96 2.4682
> 35 120 3.37045
> 35 144 3.95961
> 35 168 4.63802
> 35 192 13.3627
> 35 216 17.2143
> 35 240 17.3732
> 35 264 17.3738
>
> 37 -168 17.3738
> 37 -144 17.3738
> 37 -120 17.3738
> 37 -96 17.3738
> 37 -72 17.3738
> 37 -48 17.3479
> 37 -24 15.5378
> 37 0 4.84464
> 37 24 1.91233
> 37 48 3.19268
> 37 72 3.32899
> 37 96 3.37165
> 37 120 3.50371
> 37 144 3.2846
> 37 168 4.61725
> 37 192 13.5829
> 37 216 17.2344
> 37 240 17.3734
> 37 264 17.3738
>
> 39 -168 17.3738
> 39 -144 17.3738
> 39 -120 17.3738
> 39 -96 17.3738
> 39 -72 17.3738
> 39 -48 17.3506
> 39 -24 15.718
> 39 0 6.0774
> 39 24 3.12393
> 39 48 4.02323
> 39 72 3.53219
> 39 96 3.52273
> 39 120 4.08879
> 39 144 4.25361
> 39 168 4.74903
> 39 192 13.6482
> 39 216 17.2419
> 39 240 17.3734
> 39 264 17.3738
>
> 41 -168 17.3738
> 41 -144 17.3738
> 41 -120 17.3738
> 41 -96 17.3738
> 41 -72 17.3738
> 41 -48 17.3499
> 41 -24 15.6662
> 41 0 5.81911
> 41 24 3.75407
> 41 48 4.88836
> 41 72 4.29999
> 41 96 4.35963
> 41 120 4.48403
> 41 144 5.78017
> 41 168 6.0968
> 41 192 14.0942
> 41 216 17.2632
> 41 240 17.3735
> 41 264 17.3738
>
> 43 -168 17.3738
> 43 -144 17.3738
> 43 -120 17.3738
> 43 -96 17.3738
> 43 -72 17.3738
> 43 -48 17.3549
> 43 -24 15.966
> 43 0 7.34364
> 43 24 4.98942
> 43 48 4.95558
> 43 72 5.16925
> 43 96 5.14047
> 43 120 6.41121
> 43 144 7.94687
> 43 168 9.3565
> 43 192 15.2873
> 43 216 17.308
> 43 240 17.3736
> 43 264 17.3738
>
> 45 -168 17.3738
> 45 -144 17.3738
> 45 -120 17.3738
> 45 -96 17.3738
> 45 -72 17.3738
> 45 -48 17.3558
> 45 -24 16.0634
> 45 0 7.91329
> 45 24 5.29474
> 45 48 6.00668
> 45 72 6.8629
> 45 96 7.56553
> 45 120 9.45886
> 45 144 11.3337
> 45 168 11.754
> 45 192 15.8191
> 45 216 17.3202
> 45 240 17.3737
> 45 264 17.3738
>
> 47 -168 17.3738
> 47 -144 17.3738
> 47 -120 17.3738
> 47 -96 17.3738
> 47 -72 17.3738
> 47 -48 17.3625
> 47 -24 16.4816
> 47 0 10.261
> 47 24 7.00247
> 47 48 7.82204
> 47 72 9.93866
> 47 96 11.5356
> 47 120 13.8702
> 47 144 14.748
> 47 168 14.4067
> 47 192 16.5272
> 47 216 17.3435
> 47 240 17.3737
> 47 264 17.3738
>
> 49 -168 17.3738
> 49 -144 17.3738
> 49 -120 17.3738
> 49 -96 17.3738
> 49 -72 17.3738
> 49 -48 17.3717
> 49 -24 17.1967
> 49 0 15.8322
> 49 24 14.024
> 49 48 12.8823
> 49 72 14.9701
> 49 96 16.4567
> 49 120 16.8758
> 49 144 17.0202
> 49 168 16.9236
> 49 192 17.2506
> 49 216 17.3699
> 49 240 17.3738
> 49 264 17.3738
>
> 51 -168 17.3738
> 51 -144 17.3738
> 51 -120 17.3738
> 51 -96 17.3738
> 51 -72 17.3738
> 51 -48 17.3738
> 51 -24 17.3689
> 51 0 17.3152
> 51 24 17.0934
> 51 48 16.917
> 51 72 17.199
> 51 96 17.3461
> 51 120 17.3619
> 51 144 17.3676
> 51 168 17.3658
> 51 192 17.3717
> 51 216 17.3738
> 51 240 17.3738
> 51 264 17.3738
>
> 53 -168 17.3738
> 53 -144 17.3738
> 53 -120 17.3738
> 53 -96 17.3738
> 53 -72 17.3738
> 53 -48 17.3738
> 53 -24 17.3738
> 53 0 17.3735
> 53 24 17.3707
> 53 48 17.3685
> 53 72 17.3722
> 53 96 17.3737
> 53 120 17.3738
> 53 144 17.3738
> 53 168 17.3738
> 53 192 17.3738
> 53 216 17.3738
> 53 240 17.3738
> 53 264 17.3738
>
> 55 -168 17.3738
> 55 -144 17.3738
> 55 -120 17.3738
> 55 -96 17.3738
> 55 -72 17.3738
> 55 -48 17.3738
> 55 -24 17.3738
> 55 0 17.3738
> 55 24 17.3738
> 55 48 17.3738
> 55 72 17.3738
> 55 96 17.3738
> 55 120 17.3738
> 55 144 17.3738
> 55 168 17.3738
> 55 192 17.3738
> 55 216 17.3738
> 55 240 17.3738
> 55 264 17.3738
>
> 57 -168 17.3738
> 57 -144 17.3738
> 57 -120 17.3738
> 57 -96 17.3738
> 57 -72 17.3738
> 57 -48 17.3738
> 57 -24 17.3738
> 57 0 17.3738
> 57 24 17.3738
> 57 48 17.3738
> 57 72 17.3738
> 57 96 17.3738
> 57 120 17.3738
> 57 144 17.3738
> 57 168 17.3738
> 57 192 17.3738
> 57 216 17.3738
> 57 240 17.3738
> 57 264 17.3738
>
> This is due to the expand boundary option, I suppose, and I am wondering
> if the pmf file as it appears has a physical meaning regarding angle and
> distance values or if it must be adjusted some way, or, worst of all, it is
> meaningless.
>
> Thanks for your help,
>
> Stefano
> --
> Stefano GUGLIELMO PhD
> Assistant Professor of Medicinal Chemistry
> Department of Drug Science and Technology
> Via P. Giuria 9
> 10125 Turin, ITALY
> ph. +39 (0)11 6707678
>
>

-- 
Giacomo Fiorin
Associate Professor of Research
Institute for Computational Molecular Science (ICMS)
College of Science and Technology, Temple University
1925 North 12th Street (035-07), Room 704D
Philadelphia, PA 19122-1801
Phone: +1-215-204-4213
Scholar: http://goo.gl/Q3TBQU
Personal: http://giacomofiorin.github.io/
Lab page: https://icms.cst.temple.edu/members.html
*"As computer programmers we have a responsibility to make sure that we run
the computers instead of the computers running us."*  - Steve Oualline

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