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

Wed Sep 15 21:09:18 CEST 2010

On 2010-09-15 21.04, teklebrh at ualberta.ca wrote:
> Thank you David,
>
> So this means my result is correct! and I have to add an explanation
> that my system is hetrogeneous only.
>
> There is nothing wrong then with my system.
>
You can test the RDF normalization etc. by integrating 4 Pi r^2g(r)dr, 
that should converge to the number of particles. See manual.
> Rob
>
> Quoting "David van der Spoel" <spoel at xray.bmc.uu.se>:
>
>> 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
>> --
>> 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