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

Wed Sep 15 21:04:53 CEST 2010

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.

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
>
>