[gmx-users] Re: density vs time
nishap.patel at utoronto.ca
nishap.patel at utoronto.ca
Wed Mar 17 15:41:53 CET 2010
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" <vvchaban at gmail.com>:
>>
>> 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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