From: Stefano Guglielmo (stefano.guglielmo_at_unito.it)
Date: Mon Jul 04 2016 - 19:43:23 CDT
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
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