[gmx-users] Correction for the PBC!
Justin A. Lemkul
jalemkul at vt.edu
Tue Sep 14 20:10:45 CEST 2010
teklebrh at ualberta.ca 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 teklebrh at ualberta.ca:
>
>>
>>
>> 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" <jalemkul at vt.edu>:
>>
>>>
>>>
>>> teklebrh at ualberta.ca 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" <jalemkul at vt.edu>:
>>>>
>>>>>
>>>>>
>>>>> teklebrh at ualberta.ca 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]
>>>>>
>>>>> ========================================
>>>>> --
>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users[2]
>>>>> Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search[3] before posting!
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>>>>> interface or send it to gmx-users-request at gromacs.org.
>>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists[4]
>>>>>
>>>>>
>>>>
>>>
>>> --
>>> ========================================
>>>
>>> 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[5]
>>>
>>> ========================================
>>> --
>>> gmx-users mailing list gmx-users at gromacs.org
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>>>
>>
>>
>>
>> Links:
>> ------
>> [1] http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> [2] http://lists.gromacs.org/mailman/listinfo/gmx-users
>> [3] http://www.gromacs.org/Support/Mailing_Lists/Search
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>> [6] http://lists.gromacs.org/mailman/listinfo/gmx-users
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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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