What do you mean the value for methane? As in the charges? This is my
topology file and I am using OPLS-AA for methane.
Include forcefield parameters
#include "ffoplsaa.itp"
[ moleculetype ]
; Name nrexcl
Methane 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 opls_138 1 METH C 1 -0.24 12.011
; qtot -0.24
2 opls_140 1 METH H1 1 0.06 1.008
; qtot -0.18
3 opls_140 1 METH H2 1 0.06 1.008
; qtot -0.12
4 opls_140 1 METH H3 1 0.06 1.008
; qtot -0.06
5 opls_140 1 METH H4 1 0.06 1.008
; qtot 0.54
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 3 1
1 4 1
1 5 1
[ angles ]
; ai aj ak funct c0 c1 c2
c3
2 1 3 1
2 1 4 1
2 1 5 1
3 1 4 1
3 1 5 1
4 1 5 1
My RDF does look reasonable and the peaks are okay with the values
published earlier, but because of what I am calculating (i.e. volume),
it seems to be very sensitive and even 0.01 makes a difference.
Thanks for suggestions.
-Nisha P
Quoting "Vitaly V. Chaban" <[email protected]>:
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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