Dear Justine,
Then my guess is you don't have a PBC problem, but perhaps a
convergence problem. You're only analyzing 1 ns of data; I don't
know what implication that will have for your outcome.
I have read about this problem and some people suggested that my box
expanded a lot means I have a gas phase. I check the density It was
fine.
I have done the same kind of analysis using the same procedure for
part of the molecule and it converged very well to 1. But for the
entire surfactant it did not converge to one (approx to zero)...... Do
you think this is an artifact or else.
If I discard these values below 1 .... what is the implication? What
will be then my justification for that.
I will be happy as well if other people comment on this topic.
WHY my RDF converge to zero not 1.
Rob
Quoting "Justin A. Lemkul" <[email protected]>:
[email protected] wrote:
Dear Justine,
I have tried every thing but the g_rdf of my surfactant molecules ....
Surfactant = PAP
PAP-PAP .. RDF looks like this..
0 0
0.002 0
0.004 0
0.006 0
0.008 0
0.01 0
0.012 0
0.014 0
0.016 0
0.018 0
0.02 0
0.022 0
0.024 0
0.026 0
0.028 0
0.03 0
0.032 0
0.034 0
0.036 0
0.038 0
0.04 0
0.042 0
0.044 0
0.046 0
0.048 0
0.05 0
0.052 0
0.054 0
0.056 0
0.058 0
0.06 0
0.062 0
0.064 0
0.066 0
0.068 0
0.07 0
0.072 0
0.074 0
0.076 0
0.078 0
0.08 0
0.082 0
0.084 0
0.086 0
0.088 0
0.09 0
0.092 0
0.094 0
0.096 0
0.098 0
0.1 0
0.102 0
0.104 0
0.106 0
0.108 0
0.11 0
0.112 0
0.114 0
0.116 0
0.118 0
0.12 0
0.122 0
0.124 0.0386708
0.126 0
0.128 0
0.13 0
0.132 0
0.134 0
0.136 0
0.138 0.0312225
0.14 0
0.142 0.0294884
0.144 0
0.146 0
0.148 0
0.15 0
0.152 0
0.154 0.050144
0.156 0
0.158 0.047637
0.16 0.0464535
0.162 0.022657
0.164 0.0221076
0.166 0.0215781
0.168 0.0632021
0.17 0.0617243
0.172 0.0803955
0.174 0.0392791
0.176 0.0767833
0.178 0.112601
0.18 0.165168
0.182 0.0718038
0.184 0.12294
0.186 0.171872
0.188 0.117764
0.19 0.0988267
0.192 0.0645195
0.194 0.205385
0.196 0.17026
0.198 0.121336
0.2 0.178384
0.202 0.145723
0.204 0.257183
0.206 0.196166
0.208 0.261133
0.21 0.350562
0.212 0.2646
0.214 0.324599
0.216 0.382335
0.218 0.450424
0.22 0.491411
0.222 0.591186
0.224 0.533271
0.226 0.651932
0.228 0.834996
0.23 1.19148
0.232 1.95537
0.234 2.38904
0.236 3.52306
0.238 4.37741
0.24 5.56415
0.242 6.89399
0.244 8.25963
0.246 10.1401
0.248 10.5862
0.25 11.5687
0.252 11.9851
0.254 12.3869
0.256 11.786
0.258 11.3537
0.26 10.8894
0.262 10.1434
0.264 9.45289
0.266 8.20198
0.268 7.95582
0.27 7.26746
0.272 7.00034
0.274 6.43903
0.276 6.16654
0.278 6.10889
0.28 6.47701
0.282 6.68453
0.284 7.12153
0.286 7.97467
0.288 8.63126
0.29 9.60143
0.292 10.5722
0.294 11.6465
0.296 12.6569
0.298 14.349
0.3 15.1626
0.302 16.1753
0.304 16.5934
0.306 17.2663
0.308 18.0833
0.31 18.3891
0.312 19.2229
0.314 19.0814
0.316 19.8116
0.318 19.5628
0.32 21.2178
0.322 20.5652
0.324 21.5411
0.326 21.5295
0.328 21.4391
0.33 22.2337
0.332 22.1936
0.334 22.6958
0.336 22.5159
0.338 23.9627
0.34 24.1445
0.342 24.5645
0.344 25.3701
0.346 25.3908
0.348 26.6904
0.35 27.0803
0.352 27.5124
0.354 30.0258
0.356 30.3648
0.358 30.5508
0.36 31.3087
0.362 32.5661
0.364 33.0299
0.366 33.3802
0.368 33.9448
0.37 35.4638
0.372 36.3684
0.374 38.6968
0.376 42.1603
0.378 46.8835
0.38 55.6397
0.382 63.6524
0.384 70.6934
0.386 72.4445
0.388 68.5321
0.39 63.1321
0.392 59.9827
0.394 59.5433
0.396 59.5346
0.398 59.6736
0.4 60.1412
0.402 63.2898
0.404 68.8691
-
-
-
-
-
-
3.618 1.49702
3.62 1.49392
3.622 1.49265
3.624 1.47739
3.626 1.48502
3.628 1.49045
3.63 1.47957
3.632 1.48315
3.634 1.47226
3.636 1.47088
3.638 1.47169
3.64 1.47815
3.642 1.45689
3.644 1.44958
3.646 1.46132
3.648 1.45749
3.65 1.45743
3.652 1.45316
3.654 1.44515
3.656 1.43456
3.658 1.45053
3.66 1.42725
3.662 1.42837
3.664 1.42375
3.666 1.43557
3.668 1.41623
3.67 1.41688
3.672 1.4284
3.674 1.39468
3.676 1.41252
3.678 1.41158
3.68 1.42698
3.682 1.39971
3.684 1.40453
3.686 1.40363
3.688 1.38676
3.69 1.3831
3.692 1.39389
3.694 1.38261
3.696 1.38849
3.698 1.39562
3.7 1.37748
3.702 1.3559
3.704 1.38009
3.706 1.37901
3.708 1.36219
3.71 1.36057
3.712 1.34968
3.714 1.35544
3.716 1.35059
3.718 1.34517
3.72 1.35307
3.722 1.33468
3.724 1.33697
3.726 1.32972
3.728 1.35317
3.73 1.34359
3.732 1.33036
3.734 1.32676
3.736 1.32371
3.738 1.31825
3.74 1.30929
3.742 1.31097
3.744 1.29373
3.746 1.30557
3.748 1.31186
3.75 1.30615
3.752 1.29304
3.754 1.30105
3.756 1.28575
3.758 1.29182
3.76 1.27846
3.762 1.29297
3.764 1.27195
3.766 1.27255
3.768 1.27472
3.77 1.26995
3.772 1.26761
3.774 1.24985
3.776 1.26267
3.778 1.25907
3.78 1.25731
3.782 1.24681
3.784 1.24505
3.786 1.25134
3.788 1.24811
3.79 1.24578
3.792 1.23609
3.794 1.23061
3.796 1.22387
3.798 1.23296
3.8 1.22636
3.802 1.23006
3.804 1.19768
3.806 1.22099
3.808 1.20974
3.81 1.21327
3.812 1.20263
3.814 1.19753
3.816 1.19019
3.818 1.19533
3.82 1.19154
3.822 1.19894
3.824 1.19425
3.826 1.19786
3.828 1.18763
3.83 1.1856
3.832 1.17327
3.834 1.1841
3.836 1.1705
3.838 1.16918
3.84 1.16837
3.842 1.16476
3.844 1.16393
3.846 1.15772
3.848 1.15619
3.85 1.14672
3.852 1.15073
3.854 1.14239
3.856 1.13708
3.858 1.12996
3.86 1.14463
3.862 1.11898
3.864 1.12187
3.866 1.11642
3.868 1.12246
3.87 1.12548
3.872 1.11631
3.874 1.11326
3.876 1.10855
3.878 1.11599
3.88 1.1087
3.882 1.09331
3.884 1.09874
3.886 1.09685
3.888 1.09971
3.89 1.10151
3.892 1.09531
3.894 1.08087
3.896 1.07741
3.898 1.08176
3.9 1.06993
3.902 1.07141
3.904 1.06588
3.906 1.06933
3.908 1.06166
3.91 1.0674
3.912 1.0484
3.914 1.05787
3.916 1.0477
3.918 1.04269
3.92 1.04876
3.922 1.03885
3.924 1.04079
3.926 1.04169
3.928 1.04109
3.93 1.0364
3.932 1.03547
3.934 1.01927
3.936 1.02606
3.938 1.0213
3.94 1.02079
3.942 1.00924
3.944 1.00848
3.946 1.00971
3.948 1.01064
3.95 0.996613
3.952 0.996559
3.954 0.996959
3.956 0.998992
3.958 0.98474
3.96 0.988146
3.962 0.99238
3.964 0.998688
3.966 0.982488
3.968 0.964017
3.97 0.970145
3.972 0.974564
3.974 0.966096
3.976 0.96833
3.978 0.957817
3.98 0.960695
3.982 0.948339
3.984 0.954437
3.986 0.949187
3.988 0.949588
3.99 0.932854
3.992 0.943381
3.994 0.943342
3.996 0.935859
3.998 0.925329
4 0.930935
4.002 0.930638
4.004 0.915742
4.006 0.916356
4.008 0.914661
4.01 0.913785
4.012 0.912741
4.014 0.914998
4.016 0.915678
4.018 0.915294
4.02 0.90147
4.022 0.895573
4.024 0.897313
4.026 0.881787
4.028 0.887577
4.03 0.890193
4.032 0.892145
4.034 0.88283
4.036 0.885348
4.038 0.876876
4.04 0.872154
4.042 0.876419
4.044 0.878118
4.046 0.865789
4.048 0.870954
4.05 0.868049
4.052 0.862877
4.054 0.858095
4.056 0.851822
4.058 0.855818
4.06 0.853619
4.062 0.842873
4.064 0.84844
4.066 0.845933
4.068 0.837848
4.07 0.833639
4.072 0.837754
4.074 0.830918
4.076 0.830175
4.078 0.825299
4.08 0.818966
4.082 0.820927
4.084 0.818022
4.086 0.812026
4.088 0.804889
4.09 0.815197
4.092 0.807292
4.094 0.810965
4.096 0.800183
4.098 0.793872
4.1 0.807127
4.102 0.789674
4.104 0.795408
4.106 0.798583
4.108 0.79196
4.11 0.786059
4.112 0.787969
4.114 0.775823
4.116 0.779488
4.118 0.777093
4.12 0.781073
4.122 0.771884
4.124 0.775363
4.126 0.766022
4.128 0.766019
4.13 0.763528
4.132 0.759282
4.134 0.761387
4.136 0.750792
4.138 0.755269
4.14 0.748107
4.142 0.744142
4.144 0.741016
4.146 0.746871
4.148 0.737341
4.15 0.730139
4.152 0.727265
4.154 0.742743
4.156 0.726984
4.158 0.725515
4.16 0.711536
4.162 0.731623
4.164 0.703933
4.166 0.721472
4.168 0.716057
4.17 0.720965
4.172 0.719051
4.174 0.704044
4.176 0.701346
4.178 0.696225
4.18 0.700132
4.182 0.701525
4.184 0.697064
4.186 0.700028
4.188 0.697499
4.19 0.687055
4.192 0.677398
4.194 0.682056
4.196 0.684369
4.198 0.678339
4.2 0.673119
4.202 0.67668
4.204 0.678804
4.206 0.668657
4.208 0.666873
4.21 0.661783
4.212 0.662844
4.214 0.666264
4.216 0.664936
4.218 0.659085
4.22 0.657377
4.222 0.647065
4.224 0.643763
4.226 0.65035
4.228 0.64951
4.23 0.644331
4.232 0.642256
4.234 0.638672
4.236 0.641769
4.238 0.645202
4.24 0.637489
4.242 0.628153
4.244 0.624075
4.246 0.627562
4.248 0.624409
4.25 0.622008
4.252 0.617578
4.254 0.618082
4.256 0.616705
4.258 0.620233
4.26 0.613723
4.262 0.613542
4.264 0.606722
4.266 0.601474
4.268 0.602512
4.27 0.610145
4.272 0.603124
4.274 0.598812
4.276 0.588374
4.278 0.59133
4.28 0.586432
4.282 0.587866
4.284 0.585618
4.286 0.573144
4.288 0.57663
4.29 0.578556
4.292 0.57521
4.294 0.580931
4.296 0.56578
4.298 0.561448
4.3 0.573121
4.302 0.573457
4.304 0.563928
4.306 0.560218
4.308 0.555828
4.31 0.556358
4.312 0.563511
4.314 0.557304
4.316 0.561251
4.318 0.545093
4.32 0.550265
4.322 0.540745
4.324 0.536129
4.326 0.552832
4.328 0.548235
4.33 0.537861
4.332 0.535545
4.334 0.528127
4.336 0.535767
4.338 0.529951
4.34 0.528368
4.342 0.523278
4.344 0.520704
4.346 0.527159
4.348 0.52593
4.35 0.525731
4.352 0.519521
4.354 0.513252
4.356 0.51457
4.358 0.518719
4.36 0.510497
4.362 0.509598
4.364 0.506181
4.366 0.504419
4.368 0.497795
4.37 0.500966
4.372 0.504876
4.374 0.489321
4.376 0.507235
4.378 0.493448
4.38 0.496172
4.382 0.491397
4.384 0.482856
4.386 0.491271
4.388 0.480308
4.39 0.481918
4.392 0.488769
4.394 0.475618
4.396 0.478773
4.398 0.479026
4.4 0.476978
4.402 0.470825
4.404 0.481324
4.406 0.466229
4.408 0.46433
4.41 0.463153
4.412 0.461773
4.414 0.452375
4.416 0.457859
4.418 0.460082
4.42 0.454811
4.422 0.463698
4.424 0.45372
4.426 0.451355
4.428 0.4544
4.43 0.444576
4.432 0.445647
4.434 0.440643
4.436 0.442069
4.438 0.442747
4.44 0.437023
4.442 0.434889
4.444 0.440704
4.446 0.432446
4.448 0.432088
4.45 0.428407
4.452 0.428726
4.454 0.427902
4.456 0.426622
4.458 0.420097
4.46 0.424059
4.462 0.423266
4.464 0.425177
4.466 0.418946
4.468 0.417772
4.47 0.417076
4.472 0.413366
4.474 0.405287
4.476 0.406673
4.478 0.406363
4.48 0.400713
4.482 0.403016
4.484 0.409838
4.486 0.404124
4.488 0.398131
4.49 0.400173
4.492 0.407882
4.494 0.397001
4.496 0.396174
4.498 0.397463
4.5 0.397709
4.502 0.390852
4.504 0.386567
4.506 0.38765
4.508 0.390087
4.51 0.382283
4.512 0.375047
4.514 0.377796
4.516 0.38053
4.518 0.377125
4.52 0.376932
4.522 0.37867
4.524 0.369377
4.526 0.365101
4.528 0.372542
4.53 0.370364
4.532 0.366127
4.534 0.366403
4.536 0.363976
4.538 0.369198
4.54 0.357528
4.542 0.364936
4.544 0.356557
4.546 0.354742
4.548 0.356217
4.55 0.352334
4.552 0.356217
4.554 0.349794
4.556 0.354308
4.558 0.352529
4.56 0.349079
4.562 0.346863
4.564 0.348607
4.566 0.344551
4.568 0.336456
4.57 0.344059
4.572 0.342846
4.574 0.343857
4.576 0.342621
4.578 0.337633
4.58 0.332792
4.582 0.330428
4.584 0.335745
4.586 0.331965
4.588 0.332565
4.59 0.327592
4.592 0.324987
4.594 0.325261
4.596 0.323394
4.598 0.321757
4.6 0.320289
4.602 0.324011
4.604 0.317495
4.606 0.319709
4.608 0.31597
4.61 0.309665
4.612 0.311883
4.614 0.310811
4.616 0.309345
4.618 0.309076
4.62 0.306849
4.622 0.306059
4.624 0.302499
4.626 0.305746
4.628 0.302484
4.63 0.299231
4.632 0.300029
4.634 0.298585
4.636 0.299477
4.638 0.299858
4.64 0.296264
4.642 0.294672
4.644 0.293695
4.646 0.289712
4.648 0.290992
4.65 0.290417
4.652 0.288514
4.654 0.283104
4.656 0.283552
4.658 0.28347
4.66 0.290235
4.662 0.285285
4.664 0.277959
4.666 0.279521
4.668 0.273256
4.67 0.277063
4.672 0.276483
4.674 0.268187
4.676 0.271514
4.678 0.268644
4.68 0.271048
4.682 0.26606
4.684 0.275102
4.686 0.267121
4.688 0.266818
4.69 0.26788
4.692 0.264629
4.694 0.264184
4.696 0.267243
4.698 0.259231
4.7 0.262627
4.702 0.259008
4.704 0.256346
4.706 0.25399
4.708 0.255914
4.71 0.255821
4.712 0.254408
4.714 0.250453
4.716 0.24994
4.718 0.252659
4.72 0.248023
4.722 0.250594
4.724 0.24799
4.726 0.247123
4.728 0.24647
4.73 0.240303
4.732 0.242484
4.734 0.238625
4.736 0.239147
4.738 0.233552
4.74 0.238918
4.742 0.236821
4.744 0.234888
4.746 0.236861
4.748 0.233715
4.75 0.232752
4.752 0.23089
4.754 0.229704
4.756 0.231364
4.758 0.230899
4.76 0.231003
4.762 0.22809
4.764 0.228475
4.766 0.221141
4.768 0.228355
4.77 0.227719
4.772 0.221959
4.774 0.220529
4.776 0.217598
4.778 0.221624
4.78 0.219706
4.782 0.219037
4.784 0.221091
4.786 0.215576
4.788 0.214745
4.79 0.212482
4.792 0.214316
4.794 0.213902
4.796 0.215149
4.798 0.207367
4.8 0.212391
4.802 0.212657
4.804 0.211209
4.806 0.206088
4.808 0.205848
4.81 0.20539
4.812 0.20463
4.814 0.205654
4.816 0.201655
4.818 0.199889
4.82 0.203828
4.822 0.200193
4.824 0.203232
4.826 0.197828
4.828 0.197051
4.83 0.195867
4.832 0.197971
4.834 0.192717
4.836 0.194464
4.838 0.195964
4.84 0.193304
4.842 0.190948
4.844 0.19491
4.846 0.192267
4.848 0.193662
4.85 0.185335
4.852 0.187522
4.854 0.186923
4.856 0.185904
4.858 0.184322
4.86 0.181996
4.862 0.185581
4.864 0.18334
4.866 0.179438
4.868 0.182014
4.87 0.179545
4.872 0.180184
4.874 0.179702
4.876 0.178584
4.878 0.177543
4.88 0.179362
4.882 0.175853
4.884 0.176353
4.886 0.172697
4.888 0.173782
4.89 0.176536
4.892 0.171556
4.894 0.170033
4.896 0.170748
4.898 0.167734
4.9 0.170794
4.902 0.169994
4.904 0.169182
4.906 0.16627
4.908 0.166794
4.91 0.167013
4.912 0.165671
4.914 0.166407
4.916 0.164396
4.918 0.167214
4.92 0.164345
4.922 0.166479
It terminated with value not 1 but close to zero.... any idea on this
g_rdf -f PAP_8_Box12_HEP_EM_NPTNHPR_20ns_PBC.xtc -s
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr -b 19000 -e 20000 -o RDFPBC.xvg
Try to correct for PBC and still the same....
Then my guess is you don't have a PBC problem, but perhaps a
convergence problem. You're only analyzing 1 ns of data; I don't
know what implication that will have for your outcome.
-Justin
Regards,
Rob
Quoting [email protected]:
Dear Justine,
No, I have 20 surfactants in my system in a pure solvent and try
to see the aggregation and adsorption properties of these
molecules. I have run them for 20ns. And now start to analyze my
data.
Just in short I want to correct for periodicity! so that to get
the accurate result for my g_dist and g_rdf.
trjconv on the xxx.xtc.... Like
trjconv -f x_input.xtc -o x_out.xtc -b 19000 -e 20000 -s
x_input.tpr -pbc nojump
or I have to cluster it first.
Rob
Quoting "Justin A. Lemkul" <[email protected]>:
[email protected] wrote:
Dear Justine,
I just checked at the archive list and found out lots of information
on how to correct for PBC! And if I understood it correctly is this
the right way to follow...
"If you are trying to correct for periodicity for all species in
the system
(protein and water) then a few iterations of trjconv may be
necessary, i.e.
-center (on protein), followed by -pbc nojump or -pbc mol -ur
compact. Using
trjconv is a bit hit-or-miss, and just requires a bit of playing to
get things working how you want them."
trjconv -f xxx.xtc -o x_cluster.gro -b 19000 -e 20000 -pbc cluster
grompp -f xx.mdp -c x_cluster.gro -o x_cluster.tpr
trjconv -f xxx.xtc -o x_cluster.xtc -b 19000 -e 20000 -s
xx_cluster.tpr -pbc nojump
Then I have to do anaysis on the new .tpr and .xtc...... is that
correct....
Is this the right way to correct for periodicity... I took the idea
from you and Chris. I have done the RDF and distance measurement but
looks a bit off my RDF did not converge to 1. They recommend me to
do PBC correction on my system which is run for 20ns. I am doing the
analysis on the last 1ns (from 19-20 ns)
Without context, I have no idea if what you've done is right. The
clustering algorithm is only really useful for the formation of
clustered molecules (i.e. micelles), so if you're trying to apply it
to something else, I don't know that it will work.
-Justin
You suggestion is always helpful!
Rob
Quoting "Justin A. Lemkul" <[email protected]>:
[email protected] wrote:
Dear Gromacs,
I want to correct the periodic boundry condition before analyzing
my data, how do I perform that?
Please see trjconv -h, as well as any of the thousands of posts in
the list archive related to this topic.
-Justin
any suggest!
Rob
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin[1]
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ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
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http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin[5]
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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