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" <jalem...@vt.edu>:
Justin A. Lemkul wrote:
nishap.pa...@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
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