[gmx-users] density vs time

nishap.patel at utoronto.ca nishap.patel at utoronto.ca
Tue Mar 16 22:51:45 CET 2010


I am trying to get an rdf graph actually, and my values are very close  
to one, but not exactly one, and I was wondering if there is some  
normalization issue with g_rdf? These are my values for rdf:

   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
      0.126          0
      0.128          0
       0.13          0
      0.132          0
      0.134          0
      0.136          0
      0.138          0
       0.14          0
      0.142          0
      0.144          0
      0.146          0
      0.148          0
       0.15          0
      0.152          0
      0.154          0
      0.156          0
      0.158          0
       0.16          0
      0.162          0
      0.164          0
      0.166          0
      0.168          0
       0.17          0
      0.172          0
      0.174          0
      0.176          0
      0.178          0
       0.18          0
      0.182          0
      0.184          0
      0.186          0
      0.188          0
       0.19          0
      0.192          0
      0.194          0
      0.196          0
      0.198          0
        0.2          0
      0.202          0
      0.204          0
      0.206          0
      0.208          0
       0.21          0
      0.212          0
      0.214          0
      0.216          0
      0.218          0
       0.22          0
      0.222          0
      0.224          0
      0.226          0
      0.228          0
       0.23          0
      0.232          0
      0.234          0
      0.236          0
      0.238          0
       0.24          0
      0.242          0
      0.244          0
      0.246          0
      0.248          0
       0.25          0
      0.252          0
      0.254          0
      0.256          0
      0.258          0
       0.26          0
      0.262          0
      0.264          0
      0.266          0
      0.268 3.32195e-05
       0.27 3.27293e-05
      0.272 0.000193501
      0.274 0.000317806
      0.276 0.000689078
      0.278 0.00126578
       0.28 0.00197816
      0.282 0.00348035
      0.284 0.00653762
      0.286  0.0111138
      0.288   0.016713
       0.29  0.0238596
      0.292  0.0345034
      0.294  0.0528889
      0.296  0.0698775
      0.298  0.0933922
        0.3   0.118079
      0.302   0.156417
      0.304   0.195336
      0.306   0.242149
      0.308   0.287833
       0.31   0.351093
      0.312   0.411434
      0.314   0.473243
      0.316   0.538749
      0.318    0.61093
       0.32   0.688108
      0.322   0.756748
      0.324   0.837504
      0.326   0.914596
      0.328   0.993652
       0.33     1.0663
      0.332    1.13958
      0.334    1.21522
      0.336    1.29358
      0.338    1.35543
       0.34    1.42607
      0.342    1.49061
      0.344    1.54496
      0.346    1.59492
      0.348    1.64578
       0.35     1.6887
      0.352    1.73861
      0.354     1.7676
      0.356    1.78996
      0.358    1.82775
       0.36    1.83798
      0.362    1.84435
      0.364    1.85567
      0.366    1.86664
      0.368    1.87024
       0.37    1.86585
      0.372    1.85472
      0.374    1.84964
      0.376    1.84624
      0.378    1.82577
       0.38     1.8069
      0.382    1.78844
      0.384    1.77257
      0.386    1.75025
      0.388    1.72797
       0.39    1.69894
      0.392    1.67908
      0.394     1.6537
      0.396    1.62812
      0.398    1.60552
        0.4    1.57759
      0.402    1.55621
      0.404    1.53355
      0.406    1.49578
      0.408    1.48583
       0.41    1.45567
      0.412    1.43467
      0.414    1.41543
      0.416     1.3816
      0.418    1.36369
       0.42    1.34185
      0.422    1.31562
      0.424    1.28986
      0.426    1.27127
      0.428    1.24739
       0.43    1.23036
      0.432    1.21598
      0.434    1.20053
      0.436    1.17903
      0.438     1.1627
       0.44     1.1486
      0.442    1.12971
      0.444    1.10987
      0.446    1.10068
      0.448    1.08301
       0.45    1.06589
      0.452     1.0572
      0.454    1.03356
      0.456    1.02144
      0.458    1.01093
       0.46   0.999176
      0.462   0.983748
      0.464   0.976315
      0.466   0.960132
      0.468    0.95193
       0.47   0.940119
      0.472   0.937507
      0.474    0.92746
      0.476    0.91218
      0.478   0.905227
       0.48   0.901027
      0.482   0.883861
      0.484   0.872012
      0.486   0.871501
      0.488   0.861236
       0.49   0.855628
      0.492    0.85084
      0.494   0.846611
      0.496   0.839804
      0.498   0.832431
        0.5    0.82711
      0.502   0.820518
      0.504   0.815931
      0.506   0.805553
      0.508   0.809657
       0.51   0.802229
      0.512   0.799135
      0.514   0.794028
      0.516     0.7938
      0.518   0.789457
       0.52   0.787434
      0.522   0.785199
      0.524   0.780233
      0.526   0.777301
      0.528     0.7782
       0.53   0.780274
      0.532    0.78405
      0.534   0.779049
      0.536   0.778457
      0.538   0.777937
       0.54   0.788429
      0.542   0.781973
      0.544   0.782796
      0.546   0.788838
      0.548   0.791638
       0.55   0.794149
      0.552   0.797927
      0.554   0.799896
      0.556   0.806044
      0.558   0.806472
       0.56   0.815236
      0.562   0.822147
      0.564   0.824565
      0.566    0.82688
      0.568   0.837779
       0.57   0.839535
      0.572    0.85107
      0.574   0.859169
      0.576   0.865325
      0.578   0.876879
       0.58   0.881985
      0.582    0.89474
      0.584   0.893694
      0.586   0.904503
      0.588   0.920122
       0.59   0.930537
      0.592   0.934759
      0.594   0.946158
      0.596   0.951872
      0.598   0.962671
        0.6   0.968691
      0.602   0.976406
      0.604   0.989538
      0.606   0.994007
      0.608     1.0051
       0.61    1.01191
      0.612    1.01618
      0.614    1.02365
      0.616    1.03378
      0.618     1.0341
       0.62    1.04287
      0.622    1.04814
      0.624    1.05048
      0.626    1.05958
      0.628    1.06044
       0.63     1.0703
      0.632    1.06911
      0.634    1.07214
      0.636    1.07062
      0.638    1.07816
       0.64    1.07716
      0.642    1.07854
      0.644    1.07833
      0.646    1.08024
      0.648    1.08212
       0.65    1.07849
      0.652    1.07939
      0.654    1.08222
      0.656    1.08643
      0.658    1.07989
       0.66    1.08555
      0.662     1.0809
      0.664    1.07697
      0.666    1.07408
      0.668    1.07359
       0.67    1.07393
      0.672    1.07496
      0.674    1.07261
      0.676    1.06707
      0.678    1.06585
       0.68    1.06882
      0.682    1.06825
      0.684    1.06476
      0.686    1.06102
      0.688     1.0595
       0.69    1.05802
      0.692    1.05431
      0.694     1.0556
      0.696    1.05047
      0.698    1.04914
        0.7    1.04683
      0.702    1.04544
      0.704    1.04485
      0.706    1.04227
      0.708    1.04364
       0.71    1.03773
      0.712    1.03028
      0.714    1.03173
      0.716     1.0344
      0.718    1.03129
       0.72    1.03139
      0.722    1.02722
      0.724    1.02874
      0.726    1.02073
      0.728    1.02168
       0.73    1.01921
      0.732    1.01825
      0.734    1.02057
      0.736    1.01212
      0.738    1.01283
       0.74    1.01244
      0.742    1.01218
      0.744     1.0121
      0.746    1.00697
      0.748    1.00879
       0.75     1.0049
      0.752    1.00385
      0.754    1.00454
      0.756    1.00467
      0.758    1.00241
       0.76    1.00597
      0.762    0.99878
      0.764   0.999362
      0.766   0.997916
      0.768   0.999553
       0.77    0.99394
      0.772   0.996918
      0.774    0.99861
      0.776   0.998062
      0.778   0.995829
       0.78   0.995665
      0.782   0.991158
      0.784   0.993166
      0.786   0.993317
      0.788   0.988298
       0.79   0.992643
      0.792   0.991056
      0.794   0.987305
      0.796    0.98944
      0.798   0.989074
        0.8   0.986717
      0.802     0.9882
      0.804    0.98571
      0.806   0.987209
      0.808   0.990424
       0.81   0.987083
      0.812   0.985193
      0.814   0.985061
      0.816   0.984737
      0.818   0.984942
       0.82   0.984881
      0.822   0.985885
      0.824   0.987107
      0.826   0.982715
      0.828   0.985119
       0.83   0.987138
      0.832   0.985964
      0.834   0.986005
      0.836   0.981673
      0.838   0.982415
       0.84   0.984552
      0.842   0.985368
      0.844   0.977779
      0.846   0.980927
      0.848   0.984628
       0.85   0.989775
      0.852   0.986042
      0.854   0.984692
      0.856   0.985441
      0.858   0.986366
       0.86   0.985887
      0.862    0.98888
      0.864   0.988611
      0.866   0.989229
      0.868   0.986269
       0.87   0.987912
      0.872   0.986648
      0.874   0.990954
      0.876   0.989813
      0.878   0.990742
       0.88   0.990515
      0.882   0.986976
      0.884   0.993526
      0.886   0.991169
      0.888   0.992141
       0.89   0.990366
      0.892     0.9913
      0.894   0.995312
      0.896   0.990771
      0.898   0.992455
        0.9   0.991514
      0.902   0.993262
      0.904   0.996755
      0.906   0.995517
      0.908   0.996353
       0.91   0.991881
      0.912   0.994453
      0.914   0.995881
      0.916   0.995968
      0.918   0.998059
       0.92   0.995915
      0.922   0.996393
      0.924   0.997279
      0.926   0.997195
      0.928   0.996136
       0.93   0.999274
      0.932   0.995831
      0.934   0.995949
      0.936    1.00109
      0.938   0.998608
       0.94   0.997568
      0.942    1.00137
      0.944     1.0007
      0.946     1.0009
      0.948   0.996415
       0.95     1.0003
      0.952    1.00409
      0.954    1.00338
      0.956    1.00173
      0.958    1.00215
       0.96    1.00346
      0.962     1.0028
      0.964    1.00146
      0.966    1.00462
      0.968    1.00401
       0.97    1.00338
      0.972    1.00557
      0.974    1.00318
      0.976    1.00616
      0.978    1.00645
       0.98    1.00794
      0.982    1.00694
      0.984     1.0042
      0.986    1.00686
      0.988    1.00617
       0.99     1.0056
      0.992    1.00399
      0.994    1.00842
      0.996    1.00801
      0.998    1.00884
          1    1.00467
      1.002    1.00578
      1.004    1.00838
      1.006     1.0044
      1.008    1.00527
       1.01    1.00743
      1.012    1.00738
      1.014    1.00649
      1.016    1.00986
      1.018    1.00583
       1.02    1.00782
      1.022    1.00798
      1.024    1.00568
      1.026    1.00459
      1.028    1.00885
       1.03    1.00609
      1.032    1.00694
      1.034    1.00714
      1.036    1.00495
      1.038    1.00817
       1.04    1.00915
      1.042    1.00513
      1.044    1.00798
      1.046    1.00685
      1.048    1.00411
       1.05     1.0045
      1.052    1.00475
      1.054    1.00435
      1.056    1.00723
      1.058    1.00394
       1.06    1.00548
      1.062    1.00442
      1.064    1.00523
      1.066    1.00119
      1.068      1.005
       1.07    1.00338
      1.072    1.00677
      1.074     1.0056
      1.076    1.00191
      1.078    1.00364
       1.08    1.00201
      1.082    1.00091
      1.084    1.00444
      1.086    1.00395
      1.088    1.00019
       1.09    1.00312
      1.092    1.00105
      1.094    1.00046
      1.096    1.00009
      1.098    1.00238
        1.1   0.997774
      1.102    1.00116
      1.104   0.999177
      1.106   0.999075
      1.108    0.99965
       1.11    1.00027
      1.112   0.996616
      1.114   0.999098
      1.116   0.999091
      1.118   0.997033
       1.12   0.999598
      1.122   0.999695
      1.124   0.998096
      1.126   0.998339
      1.128   0.997582
       1.13   0.998625
      1.132   0.996005
      1.134    1.00085
      1.136   0.998892
      1.138   0.998049
       1.14   0.997158
      1.142   0.997571
      1.144   0.999554
      1.146   0.996233
      1.148    1.00116
       1.15   0.998207
      1.152   0.998212
      1.154   0.998348
      1.156   0.996611
      1.158   0.997155
       1.16   0.995056
      1.162   0.995144
      1.164   0.996621
      1.166   0.999163
      1.168   0.994951
       1.17   0.997941
      1.172   0.997855
      1.174   0.997045
      1.176   0.996823
      1.178   0.996131
       1.18   0.996537
      1.182   0.997731
      1.184   0.996762
      1.186    1.00028
      1.188    1.00151
       1.19   0.996905
      1.192   0.998277
      1.194   0.998658
      1.196   0.997687
      1.198   0.998443
        1.2   0.998217
      1.202   0.998213
      1.204   0.997245
      1.206   0.999272
      1.208   0.995826
       1.21   0.998851
      1.212   0.998046
      1.214   0.997038
      1.216   0.998801
      1.218   0.998077
       1.22   0.998735
      1.222    1.00081
      1.224    1.00086
      1.226   0.998978
      1.228   0.997882
       1.23    1.00016
      1.232    1.00034
      1.234   0.999402
      1.236   0.999584
      1.238   0.998325
       1.24   0.998195
      1.242   0.999467
      1.244   0.999988
      1.246   0.999602
      1.248      1.001
       1.25     1.0017
      1.252    1.00054
      1.254    1.00049
      1.256    1.00116
      1.258    1.00127
       1.26    1.00187
      1.262     1.0013
      1.264    1.00039
      1.266    1.00169
      1.268    1.00177
       1.27     1.0021
      1.272    1.00309
      1.274    1.00321
      1.276    1.00184
      1.278    1.00126
       1.28    1.00054
      1.282   0.999957
      1.284    1.00404
      1.286    1.00117
      1.288    1.00093
       1.29    1.00401
      1.292    1.00123
      1.294    1.00174
      1.296     1.0012
      1.298    1.00145
        1.3     1.0011
      1.302    1.00058
      1.304    1.00468
      1.306    1.00386
      1.308     1.0001
       1.31    1.00268
      1.312    1.00259
      1.314    1.00207
      1.316    1.00328
      1.318    1.00197
       1.32    1.00273
      1.322    1.00324
      1.324   0.999678
      1.326   0.999545
      1.328    1.00222
       1.33    1.00195
      1.332   0.999959
      1.334    1.00205
      1.336    1.00177
      1.338    1.00262
       1.34    1.00283
      1.342    1.00122
      1.344     1.0023
      1.346    1.00139
      1.348    1.00301
       1.35    1.00127
      1.352    1.00175
      1.354    1.00334
      1.356     1.0008
      1.358     1.0003
       1.36    1.00191
      1.362    1.00233
      1.364    1.00145
      1.366    1.00262
      1.368    1.00097
       1.37    1.00153
      1.372   0.999986
      1.374    1.00143
      1.376    1.00064
      1.378    1.00249
       1.38    1.00159
      1.382    1.00047
      1.384   0.999746
      1.386    1.00118
      1.388   0.999218
       1.39   0.999708
      1.392    1.00165
      1.394    1.00004
      1.396   0.999487
      1.398   0.999952
        1.4    1.00119
      1.402    1.00174
      1.404    1.00025
      1.406     1.0022
      1.408   0.999813
       1.41   0.999993
      1.412    1.00085
      1.414    1.00179
      1.416   0.999285
      1.418     1.0006
       1.42    1.00155
      1.422    1.00152
      1.424   0.999442
      1.426   0.999406
      1.428    1.00012
       1.43     1.0008
      1.432   0.999421
      1.434   0.999454
      1.436   0.999732
      1.438    1.00037
       1.44    1.00073
      1.442   0.999739
      1.444    1.00011
      1.446   0.999256
      1.448     1.0008
       1.45    1.00002
      1.452    1.00107
      1.454    1.00038
      1.456   0.999125
      1.458    1.00215
       1.46   0.999675
      1.462          1
      1.464   0.999633
      1.466    1.00094
      1.468    1.00111
       1.47   0.999618
      1.472   0.998297
      1.474   0.999693
      1.476    1.00042
      1.478    1.00028
       1.48    1.00272
      1.482    1.00026

Near the end, the values are fluctuating around one. The reason I was  
trying to get density values was may be to try an understand if the  
density computed by gromacs is different for just water system and  
water+one methane system (i.e. gromacs calculates the density using  
the box and total number of molecules in the box, which would be fine  
for water system but for methane+water it would slightly be a little  
different, no?) and may be normalize my rdf using the difference in  
the density factor. Does that make sense?

-Nisha



Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

>
>
> Justin A. Lemkul wrote:
>>
>>
>> nishap.patel at utoronto.ca wrote:
>>> Hello,
>>>
>>>    I am simulating one methane molecule in 899 water molecues in   
>>> the box size of 3 3 3 nm (27nm^3). I would like to determine   
>>> density vs time. Is there a way I can do that? I am running my   
>>> simulation at constant Volume i.e. no pressure coupling. I tried   
>>> using g_density but it gives me density vs box(nm).
>>>
>>> Any suggestions would be useful.
>>>
>>
>> g_energy stores density information, except in the case of an NVT   
>> ensemble.  If your box is fixed, so too is the density.
>>
>
> Edit: g_energy prints density, provided it is contained within the .edr
> file. In your case, it will not be.
>
> -Justin
>
> -- 
> ========================================
>
> 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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Nisha Patel
MSc Candidate
Leslie Dan Faculty of Pharmacy
Department of Pharmaceutical Sciences
144 College Street
Room 1172
Toronto, ON
M5S 3M2
Canada
Telephone: 416-978-1536




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