[gmx-users] Re: density vs time
Vitaly V. Chaban
vvchaban at gmail.com
Wed Mar 17 07:29:31 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
If you don't use barostat, the density of the system is fixed by
yourself. g_rdf uses it to calculate the average particle density in
the box. Your rdf seems very reasonable as for me.
This is another question how you selected the concrete value for
methane in water system...
--
Dr. Vitaly Chaban
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