hi david,
I tried to use two different index files,
one for atoms and another for molecules,
because documentation doesn't specify
which one I should use. the command line
was the same in both cases:
g_potential -f water.xtc -s water.tpr -n index.ndx -sl 500
g_potential asks "how many groups?" and
I answered "1" since my systems has water
molecules, nothing else.
results are different depending on the index
file I choose but I still get an ever increasing
potential across my simulation box. see potential
files attached: potential1.xvg (atoms in index
file) and potential2.xvg (molecules in index file)
I also calculated the potential in another system
with one organic monolayer on each side of the
water film and got similar (strange) results.
I hope it helps,
andre'
/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
Dr. Andre' Farias de Moura
/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
Laboratorio de Quimica Teorica
Universidade Federal de Sao Carlos
Sao Carlos - SP - Brasil
/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
Endereco Atual
Grupo de Quimica Quantica
Instituto de Quimica de Sao Carlos
Universidade de Sao Paulo
Sao Carlos - SP - Brasil
Telefone: 55-16-3373-8055
/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
On Fri, 6 Aug 2004, David van der Spoel wrote:
> On Thu, 5 Aug 2004, Andre Farias de Moura wrote:
>
> >
> >hi david,
> >
> >I've checked both and don't think this is the problem,
> >the density profile shows an interfacial region less
> >than 0.5 nm thick and there is no overall movement.
> >
> >my simulation system contains a 6.0 nm water slab in a
> >50 nm box (z direction), I'm sending you my potential
> >files to clarify what I mean. I got these files using:
> >
> >g_potential -f water.xtc -s water.tpr -n index.ndx -sl 50
> What's in your index file?
>
>
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>
-------------- next part --------------
# This file was created by g_potential
# which is part of G R O M A C S:
# GROup of MAchos and Cynical Suckers
# All this happened at: Fri Aug 6 09:27:04 2004
#
@ title "Electrostatic Potential"
@ xaxis label "Box (nm)"
@ yaxis label "Potential (V)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "system"
0 -0
0.1 0.0411168
0.2 0.162617
0.3 0.330546
0.4 0.490913
0.5 0.637025
0.6 0.785713
0.7 0.935845
0.8 1.08166
0.9 1.22665
1 1.38046
1.1 1.5358
1.2 1.68338
1.3 1.826
1.4 1.96931
1.5 2.11343
1.6 2.2548
1.7 2.39868
1.8 2.54882
1.9 2.70158
2 2.85065
2.1 2.99691
2.2 3.14299
2.3 3.28565
2.4 3.43127
2.5 3.58283
2.6 3.73717
2.7 3.89131
2.8 4.04278
2.9 4.19376
3 4.34329
3.1 4.49326
3.2 4.65047
3.3 4.80959
3.4 4.96239
3.5 5.11189
3.6 5.26209
3.7 5.41688
3.8 5.57304
3.9 5.72938
4 5.88436
4.1 6.03204
4.2 6.17438
4.3 6.31775
4.4 6.46587
4.5 6.61616
4.6 6.76779
4.7 6.92201
4.8 7.0768
4.9 7.2292
5 7.37849
5.1 7.52639
5.2 7.67898
5.3 7.83111
5.4 7.97383
5.5 8.111
5.6 8.2546
5.7 8.44391
5.8 8.7145
5.9 9.03926
6 9.34368
6.1 9.57783
6.2 9.75392
6.3 9.90751
6.4 10.0571
6.5 10.206
6.6 10.3549
6.7 10.5038
6.8 10.6526
6.9 10.8015
7 10.9504
7.1 11.0993
7.2 11.2482
7.3 11.397
7.4 11.5459
7.5 11.6948
7.6 11.8437
7.7 11.9926
7.8 12.1415
7.9 12.2904
8 12.4393
8.1 12.5881
8.2 12.737
8.3 12.8859
8.4 13.0348
8.5 13.1837
8.6 13.3326
8.7 13.4814
8.8 13.6303
8.9 13.7792
9 13.9281
9.1 14.077
9.2 14.2259
9.3 14.3748
9.4 14.5237
9.5 14.6726
9.6 14.8214
9.7 14.9703
9.8 15.1192
9.9 15.2681
10 15.417
10.1 15.5659
10.2 15.7148
10.3 15.8637
10.4 16.0126
10.5 16.1614
10.6 16.3103
10.7 16.4592
10.8 16.6081
10.9 16.757
11 16.9059
11.1 17.0548
11.2 17.2037
11.3 17.3526
11.4 17.5014
11.5 17.6503
11.6 17.7993
11.7 17.9482
11.8 18.097
11.9 18.2459
12 18.3948
12.1 18.5437
12.2 18.6926
12.3 18.8415
12.4 18.9904
12.5 19.1393
12.6 19.2882
12.7 19.437
12.8 19.5859
12.9 19.7348
13 19.8837
13.1 20.0326
13.2 20.1815
13.3 20.3303
13.4 20.4792
13.5 20.6281
13.6 20.777
13.7 20.9259
13.8 21.0747
13.9 21.2236
14 21.3725
14.1 21.5214
14.2 21.6703
14.3 21.8192
14.4 21.9681
14.5 22.117
14.6 22.2658
14.7 22.4147
14.8 22.5636
14.9 22.7125
15 22.8614
15.1 23.0102
15.2 23.1591
15.3 23.3079
15.4 23.4568
15.5 23.6057
15.6 23.7546
15.7 23.9035
15.8 24.0524
15.9 24.2013
16 24.3502
16.1 24.4991
16.2 24.648
16.3 24.7969
16.4 24.9458
16.5 25.0947
16.6 25.2436
16.7 25.3925
16.8 25.5414
16.9 25.6903
17 25.8392
17.1 25.9881
17.2 26.137
17.3 26.2858
17.4 26.4347
17.5 26.5836
17.6 26.7325
17.7 26.8814
17.8 27.0303
17.9 27.1791
18 27.328
18.1 27.4769
18.2 27.6258
18.3 27.7747
18.4 27.9236
18.5 28.0725
18.6 28.2214
18.7 28.3703
18.8 28.5192
18.9 28.668
19 28.8169
19.1 28.9658
19.2 29.1147
19.3 29.2636
19.4 29.4125
19.5 29.5614
19.6 29.7103
19.7 29.8592
19.8 30.0081
19.9 30.157
20 30.3058
20.1 30.4547
20.2 30.6036
20.3 30.7525
20.4 30.9014
20.5 31.0503
20.6 31.1992
20.7 31.3481
20.8 31.497
20.9 31.6459
21 31.7947
21.1 31.9436
21.2 32.0925
21.3 32.2414
21.4 32.3903
21.5 32.5392
21.6 32.688
21.7 32.8369
21.8 32.9858
21.9 33.1347
22 33.2836
22.1 33.4324
22.2 33.5813
22.3 33.7302
22.4 33.8791
22.5 34.028
22.6 34.1768
22.7 34.3257
22.8 34.4746
22.9 34.6235
23 34.7724
23.1 34.9213
23.2 35.0702
23.3 35.2191
23.4 35.368
23.5 35.5168
23.6 35.6657
23.7 35.8146
23.8 35.9635
23.9 36.1124
24 36.2612
24.1 36.4101
24.2 36.559
24.3 36.7079
24.4 36.8568
24.5 37.0056
24.6 37.1545
24.7 37.3034
24.8 37.4523
24.9 37.6012
25 37.75
25.1 37.8989
25.2 38.0478
25.3 38.1968
25.4 38.3456
25.5 38.4945
25.6 38.6434
25.7 38.7923
25.8 38.9412
25.9 39.0901
26 39.239
26.1 39.3878
26.2 39.5367
26.3 39.6856
26.4 39.8344
26.5 39.9833
26.6 40.1322
26.7 40.2811
26.8 40.43
26.9 40.5788
27 40.7277
27.1 40.8766
27.2 41.0255
27.3 41.1743
27.4 41.3232
27.5 41.4721
27.6 41.621
27.7 41.7698
27.8 41.9187
27.9 42.0676
28 42.2165
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28.2 42.5144
28.3 42.6633
28.4 42.8121
28.5 42.961
28.6 43.1099
28.7 43.2588
28.8 43.4077
28.9 43.5566
29 43.7055
29.1 43.8544
29.2 44.0032
29.3 44.1521
29.4 44.301
29.5 44.4499
29.6 44.5988
29.7 44.7476
29.8 44.8965
29.9 45.0454
30 45.1943
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30.2 45.492
30.3 45.6409
30.4 45.7897
30.5 45.9386
30.6 46.0875
30.7 46.2364
30.8 46.3853
30.9 46.5342
31 46.6831
31.1 46.832
31.2 46.9809
31.3 47.1298
31.4 47.2787
31.5 47.4275
31.6 47.5764
31.7 47.7253
31.8 47.8742
31.9 48.0231
32 48.172
32.1 48.3209
32.2 48.4697
32.3 48.6186
32.4 48.7675
32.5 48.9164
32.6 49.0653
32.7 49.2142
32.8 49.3631
32.9 49.5119
33 49.6608
33.1 49.8096
33.2 49.9585
33.3 50.1074
33.4 50.2563
33.5 50.4052
33.6 50.5541
33.7 50.703
33.8 50.8518
33.9 51.0007
34 51.1496
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34.2 51.4475
34.3 51.5964
34.4 51.7453
34.5 51.8942
34.6 52.0431
34.7 52.192
34.8 52.3408
34.9 52.4897
35 52.6386
35.1 52.7874
35.2 52.9363
35.3 53.0852
35.4 53.2341
35.5 53.383
35.6 53.5319
35.7 53.6807
35.8 53.8296
35.9 53.9785
36 54.1274
36.1 54.2763
36.2 54.4252
36.3 54.5741
36.4 54.723
36.5 54.8719
36.6 55.0208
36.7 55.1696
36.8 55.3185
36.9 55.4674
37 55.6163
37.1 55.7652
37.2 55.9141
37.3 56.063
37.4 56.2119
37.5 56.3608
37.6 56.5097
37.7 56.6586
37.8 56.8074
37.9 56.9563
38 57.1052
38.1 57.2541
38.2 57.4029
38.3 57.5518
38.4 57.7007
38.5 57.8496
38.6 57.9985
38.7 58.1474
38.8 58.2963
38.9 58.4452
39 58.5941
39.1 58.743
39.2 58.8919
39.3 59.0408
39.4 59.1896
39.5 59.3385
39.6 59.4874
39.7 59.6363
39.8 59.7852
39.9 59.9341
40 60.083
40.1 60.2319
40.2 60.3808
40.3 60.5297
40.4 60.6786
40.5 60.8275
40.6 60.9764
40.7 61.1253
40.8 61.2742
40.9 61.423
41 61.5719
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41.2 61.8697
41.3 62.0186
41.4 62.1675
41.5 62.3164
41.6 62.4653
41.7 62.6142
41.8 62.7632
41.9 62.9121
42 63.061
42.1 63.2099
42.2 63.3588
42.3 63.5078
42.4 63.6567
42.5 63.8056
42.6 63.9545
42.7 64.1034
42.8 64.2523
42.9 64.4013
43 64.5502
43.1 64.6991
43.2 64.848
43.3 64.9969
43.4 65.1458
43.5 65.2947
43.6 65.4436
43.7 65.5924
43.8 65.7413
43.9 65.8902
44 66.039
44.1 66.1879
44.2 66.3368
44.3 66.4857
44.4 66.6346
44.5 66.7835
44.6 66.9324
44.7 67.0813
44.8 67.2302
44.9 67.3791
45 67.528
45.1 67.6769
45.2 67.8258
45.3 67.9747
45.4 68.1236
45.5 68.2725
45.6 68.4214
45.7 68.5703
45.8 68.7191
45.9 68.868
46 69.0169
46.1 69.1658
46.2 69.3147
46.3 69.4636
46.4 69.6125
46.5 69.7614
46.6 69.9103
46.7 70.0592
46.8 70.2081
46.9 70.357
47 70.5059
47.1 70.6548
47.2 70.8037
47.3 70.9525
47.4 71.1013
47.5 71.2502
47.6 71.3991
47.7 71.548
47.8 71.6969
47.9 71.8458
48 71.9947
48.1 72.1436
48.2 72.2925
48.3 72.4415
48.4 72.5904
48.5 72.7393
48.6 72.8881
48.7 73.037
48.8 73.1859
48.9 73.3347
49 73.4836
49.1 73.6325
49.2 73.7814
49.3 73.9302
49.4 74.0789
49.5 74.2266
49.6 74.3667
49.7 74.4788
49.8 74.5327
49.9 74.5248
-------------- next part --------------
# This file was created by g_potential
# which is part of G R O M A C S:
# Getting the Right Output Means no Artefacts in Calculating Stuff
# All this happened at: Fri Aug 6 09:27:38 2004
#
@ title "Electrostatic Potential"
@ xaxis label "Box (nm)"
@ yaxis label "Potential (V)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "system"
0 -0
0.1 0.0163993
0.2 0.0642188
0.3 0.133506
0.4 0.194283
0.5 0.233195
0.6 0.272403
0.7 0.31572
0.8 0.348332
0.9 0.370877
1 0.393573
1.1 0.42292
1.2 0.456152
1.3 0.486919
1.4 0.518485
1.5 0.559126
1.6 0.609533
1.7 0.662058
1.8 0.714244
1.9 0.766293
2 0.812925
2.1 0.859002
2.2 0.903423
2.3 0.940909
2.4 0.980949
2.5 1.02461
2.6 1.06435
2.7 1.09734
2.8 1.12899
2.9 1.16773
3 1.21637
3.1 1.27413
3.2 1.34047
3.3 1.40789
3.4 1.47133
3.5 1.53768
3.6 1.60572
3.7 1.66911
3.8 1.72788
3.9 1.78572
4 1.84418
4.1 1.89726
4.2 1.94371
4.3 1.99059
4.4 2.03595
4.5 2.07575
4.6 2.11608
4.7 2.15676
4.8 2.18883
4.9 2.21847
5 2.25318
5.1 2.28531
5.2 2.31556
5.3 2.3503
5.4 2.38458
5.5 2.41528
5.6 2.45208
5.7 2.50541
5.8 2.57982
5.9 2.66811
6 2.75057
6.1 2.81526
6.2 2.86586
6.3 2.91087
6.4 2.95496
6.5 2.99887
6.6 3.04279
6.7 3.08671
6.8 3.13062
6.9 3.17454
7 3.21846
7.1 3.26238
7.2 3.30629
7.3 3.35021
7.4 3.39413
7.5 3.43804
7.6 3.48196
7.7 3.52588
7.8 3.5698
7.9 3.61371
8 3.65763
8.1 3.70155
8.2 3.74546
8.3 3.78938
8.4 3.8333
8.5 3.87722
8.6 3.92113
8.7 3.96505
8.8 4.00897
8.9 4.05288
9 4.0968
9.1 4.14072
9.2 4.18464
9.3 4.22855
9.4 4.27247
9.5 4.31639
9.6 4.3603
9.7 4.40422
9.8 4.44814
9.9 4.49206
10 4.53597
10.1 4.57989
10.2 4.62381
10.3 4.66773
10.4 4.71164
10.5 4.75556
10.6 4.79948
10.7 4.8434
10.8 4.88731
10.9 4.93123
11 4.97515
11.1 5.01907
11.2 5.06298
11.3 5.1069
11.4 5.15082
11.5 5.19474
11.6 5.23865
11.7 5.28257
11.8 5.32649
11.9 5.37041
12 5.41432
12.1 5.45824
12.2 5.50216
12.3 5.54607
12.4 5.58999
12.5 5.63391
12.6 5.67783
12.7 5.72174
12.8 5.76566
12.9 5.80958
13 5.8535
13.1 5.89741
13.2 5.94133
13.3 5.98525
13.4 6.02917
13.5 6.07308
13.6 6.117
13.7 6.16092
13.8 6.20484
13.9 6.24875
14 6.29267
14.1 6.33659
14.2 6.38051
14.3 6.42442
14.4 6.46834
14.5 6.51226
14.6 6.55618
14.7 6.60009
14.8 6.64401
14.9 6.68793
15 6.73185
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15.2 6.81968
15.3 6.8636
15.4 6.90752
15.5 6.95143
15.6 6.99535
15.7 7.03927
15.8 7.08319
15.9 7.1271
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16.1 7.21494
16.2 7.25885
16.3 7.30277
16.4 7.34669
16.5 7.39061
16.6 7.43453
16.7 7.47844
16.8 7.52236
16.9 7.56628
17 7.61019
17.1 7.65411
17.2 7.69803
17.3 7.74195
17.4 7.78586
17.5 7.82978
17.6 7.8737
17.7 7.91762
17.8 7.96153
17.9 8.00545
18 8.04937
18.1 8.09329
18.2 8.1372
18.3 8.18112
18.4 8.22504
18.5 8.26896
18.6 8.31287
18.7 8.35679
18.8 8.40071
18.9 8.44463
19 8.48854
19.1 8.53246
19.2 8.57638
19.3 8.6203
19.4 8.66421
19.5 8.70813
19.6 8.75205
19.7 8.79597
19.8 8.83988
19.9 8.8838
20 8.92772
20.1 8.97164
20.2 9.01555
20.3 9.05947
20.4 9.10339
20.5 9.1473
20.6 9.19122
20.7 9.23514
20.8 9.27905
20.9 9.32297
21 9.36689
21.1 9.41081
21.2 9.45472
21.3 9.49864
21.4 9.54256
21.5 9.58647
21.6 9.63039
21.7 9.67431
21.8 9.71822
21.9 9.76214
22 9.80606
22.1 9.84997
22.2 9.89389
22.3 9.93781
22.4 9.98173
22.5 10.0256
22.6 10.0696
22.7 10.1135
22.8 10.1574
22.9 10.2013
23 10.2452
23.1 10.2891
23.2 10.3331
23.3 10.377
23.4 10.4209
23.5 10.4648
23.6 10.5087
23.7 10.5526
23.8 10.5966
23.9 10.6405
24 10.6844
24.1 10.7283
24.2 10.7722
24.3 10.8161
24.4 10.8601
24.5 10.904
24.6 10.9479
24.7 10.9918
24.8 11.0357
24.9 11.0796
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25.2 11.2114
25.3 11.2553
25.4 11.2992
25.5 11.3431
25.6 11.3871
25.7 11.431
25.8 11.4749
25.9 11.5188
26 11.5627
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26.2 11.6506
26.3 11.6945
26.4 11.7384
26.5 11.7823
26.6 11.8262
26.7 11.8702
26.8 11.9141
26.9 11.958
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27.2 12.0897
27.3 12.1337
27.4 12.1776
27.5 12.2215
27.6 12.2654
27.7 12.3093
27.8 12.3532
27.9 12.3972
28 12.4411
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28.3 12.5728
28.4 12.6167
28.5 12.6607
28.6 12.7046
28.7 12.7485
28.8 12.7924
28.9 12.8363
29 12.8802
29.1 12.9242
29.2 12.9681
29.3 13.012
29.4 13.0559
29.5 13.0998
29.6 13.1437
29.7 13.1877
29.8 13.2316
29.9 13.2755
30 13.3194
30.1 13.3633
30.2 13.4072
30.3 13.4512
30.4 13.4951
30.5 13.539
30.6 13.5829
30.7 13.6268
30.8 13.6707
30.9 13.7147
31 13.7586
31.1 13.8025
31.2 13.8464
31.3 13.8903
31.4 13.9342
31.5 13.9782
31.6 14.0221
31.7 14.066
31.8 14.1099
31.9 14.1538
32 14.1977
32.1 14.2417
32.2 14.2856
32.3 14.3295
32.4 14.3734
32.5 14.4173
32.6 14.4612
32.7 14.5052
32.8 14.5491
32.9 14.593
33 14.6369
33.1 14.6808
33.2 14.7248
33.3 14.7687
33.4 14.8126
33.5 14.8565
33.6 14.9004
33.7 14.9443
33.8 14.9883
33.9 15.0322
34 15.0761
34.1 15.12
34.2 15.1639
34.3 15.2078
34.4 15.2518
34.5 15.2957
34.6 15.3396
34.7 15.3835
34.8 15.4274
34.9 15.4713
35 15.5153
35.1 15.5592
35.2 15.6031
35.3 15.647
35.4 15.6909
35.5 15.7348
35.6 15.7788
35.7 15.8227
35.8 15.8666
35.9 15.9105
36 15.9544
36.1 15.9983
36.2 16.0423
36.3 16.0862
36.4 16.1301
36.5 16.174
36.6 16.2179
36.7 16.2618
36.8 16.3058
36.9 16.3497
37 16.3936
37.1 16.4375
37.2 16.4814
37.3 16.5253
37.4 16.5693
37.5 16.6132
37.6 16.6571
37.7 16.701
37.8 16.7449
37.9 16.7888
38 16.8328
38.1 16.8767
38.2 16.9206
38.3 16.9645
38.4 17.0084
38.5 17.0523
38.6 17.0963
38.7 17.1402
38.8 17.1841
38.9 17.228
39 17.2719
39.1 17.3158
39.2 17.3598
39.3 17.4037
39.4 17.4476
39.5 17.4915
39.6 17.5354
39.7 17.5793
39.8 17.6233
39.9 17.6672
40 17.7111
40.1 17.755
40.2 17.7989
40.3 17.8429
40.4 17.8868
40.5 17.9307
40.6 17.9746
40.7 18.0185
40.8 18.0624
40.9 18.1064
41 18.1503
41.1 18.1942
41.2 18.2381
41.3 18.282
41.4 18.3259
41.5 18.3699
41.6 18.4138
41.7 18.4577
41.8 18.5016
41.9 18.5455
42 18.5894
42.1 18.6334
42.2 18.6773
42.3 18.7212
42.4 18.7651
42.5 18.809
42.6 18.8529
42.7 18.8969
42.8 18.9408
42.9 18.9847
43 19.0286
43.1 19.0725
43.2 19.1164
43.3 19.1604
43.4 19.2043
43.5 19.2482
43.6 19.2921
43.7 19.336
43.8 19.3799
43.9 19.4239
44 19.4678
44.1 19.5117
44.2 19.5556
44.3 19.5995
44.4 19.6434
44.5 19.6874
44.6 19.7313
44.7 19.7752
44.8 19.8191
44.9 19.863
45 19.9069
45.1 19.9509
45.2 19.9948
45.3 20.0387
45.4 20.0826
45.5 20.1265
45.6 20.1704
45.7 20.2144
45.8 20.2583
45.9 20.3022
46 20.3461
46.1 20.39
46.2 20.434
46.3 20.4779
46.4 20.5218
46.5 20.5657
46.6 20.6096
46.7 20.6535
46.8 20.6975
46.9 20.7414
47 20.7853
47.1 20.8292
47.2 20.8731
47.3 20.917
47.4 20.961
47.5 21.0049
47.6 21.0488
47.7 21.0927
47.8 21.1366
47.9 21.1805
48 21.2245
48.1 21.2684
48.2 21.3123
48.3 21.3562
48.4 21.4001
48.5 21.444
48.6 21.488
48.7 21.5319
48.8 21.5758
48.9 21.6197
49 21.6636
49.1 21.7075
49.2 21.7514
49.3 21.7953
49.4 21.8392
49.5 21.8827
49.6 21.9232
49.7 21.9531
49.8 21.9623
49.9 21.9513