[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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