[gmx-users] RDF converge to zero than 1, why?

David van der Spoel spoel at xray.bmc.uu.se
Wed Sep 15 20:43:30 CEST 2010


On 2010-09-15 20.34, teklebrh at ualberta.ca wrote:
>
> 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.

because your system is not homogeneous.

>
> Rob
>
>
>
>
>
>
>
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>
>>
>>
>> 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!
>>>>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>>>>> 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
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users[6]
>>>>> Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search[7] before posting!
>>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>>> interface or send it to gmx-users-request at gromacs.org.
>>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists[8]
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>> 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
>>>> [4] http://www.gromacs.org/Support/Mailing_Lists
>>>> [5] http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>> [6] http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> [7] http://www.gromacs.org/Support/Mailing_Lists/Search
>>>> [8] http://www.gromacs.org/Support/Mailing_Lists
>>>
>>
>> --
>> ========================================
>>
>> 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
>>
>> ========================================
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se



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