Dear Amber Users,
I am using ptraj to calculate Radial distribution function. I would like
to analyze which part of the organic solvent molecule interacts with
protein residues (1-129).
I used the following command to calculate RDF
trajin MD3.crd
radial md3_hyd 0.05 40 :UNK.C4,C5,C6 :1-129 closest (default density of
water 0.033)
In another case I used density of solvent molecule
radial md3_hyd 0.05 40 :UNK.C4,C5,C6 :1-129 closest density 0.001
I repeated same calculation without the keyword closest. Results are
very different in closest as well as no closest. Also RDF does not
converge to 1. It becomes zero finally. I would like to understand why
RDF does not converge to 1, or how it normalize the values. I have
pasted the output (output_standard.xmgr) of these four runs for your
kind information.
I am looking forward for your suggestion and kind help.
Thanking you
Regards
Abdul Rajjak
0.033 no closest
0.033 closest
0.001 no closest
0.001 closest
bin
hist
occupancy
0.25
0
0
0.25
0
0
0.25
0
0
0.25
0
0
0.75
0
0
0.75
0
0
0.75
0
0
0.75
0
0
1.25
0
0
1.25
0
0
1.25
0
0
1.25
0
0
1.75
0
0
1.75
0
0
1.75
0
0
1.75
0
0
2.25
0
0
2.25
0.002
0.003
2.25
0
0
2.25
0.079
0.003
2.75
0.001
0.001
2.75
1.086
1.734
2.75
0.019
0.001
2.75
36.33
1.734
3.25
0.004
0.01
3.25
4.972
12.794
3.25
0.135
0.01
3.25
166.337
12.794
3.75
0.009
0.038
3.75
4.098
24.926
3.75
0.317
0.038
3.75
137.1
24.926
4.25
0.012
0.084
4.25
2.397
34.039
4.25
0.408
0.084
4.25
80.202
34.039
4.75
0.014
0.15
4.75
1.788
42.527
4.75
0.466
0.15
4.75
59.82
42.527
5.25
0.015
0.235
5.25
1.311
50.126
5.25
0.486
0.235
5.25
43.845
50.126
5.75
0.016
0.346
5.75
1.264
58.919
5.75
0.535
0.346
5.75
42.302
58.919
6.25
0.017
0.488
6.25
1.14
68.286
6.25
0.581
0.488
6.25
38.143
68.286
6.75
0.019
0.672
6.75
1.012
77.987
6.75
0.64
0.672
6.75
33.873
77.987
7.25
0.021
0.908
7.25
0.851
87.397
7.25
0.715
0.908
7.25
28.482
87.397
7.75
0.023
1.202
7.75
0.684
96.033
7.75
0.778
1.202
7.75
22.875
96.033
8.25
0.025
1.557
8.25
0.582
104.367
8.25
0.83
1.557
8.25
19.482
104.367
8.75
0.026
1.982
8.75
0.532
112.928
8.75
0.884
1.982
8.75
17.79
112.928
9.25
0.028
2.482
9.25
0.49
121.737
9.25
0.929
2.482
9.25
16.382
121.737
9.75
0.029
3.056
9.75
0.454
130.808
9.75
0.962
3.056
9.75
15.184
130.808
10.25
0.03
3.711
10.25
0.434
140.384
10.25
0.992
3.711
10.25
14.504
140.384
10.75
0.031
4.453
10.75
0.411
150.381
10.75
1.021
4.453
10.75
13.766
150.381
11.25
0.032
5.294
11.25
0.403
161.102
11.25
1.058
5.294
11.25
13.48
161.102
11.75
0.033
6.245
11.75
0.385
172.281
11.75
1.097
6.245
11.75
12.885
172.281
12.25
0.034
7.321
12.25
0.35
183.326
12.25
1.14
7.321
12.25
11.712
183.326
12.75
0.035
8.527
12.75
0.317
194.145
12.75
1.181
8.527
12.75
10.591
194.145
13.25
0.037
9.876
13.25
0.288
204.758
13.25
1.222
9.876
13.25
9.62
204.758
13.75
0.038
11.37
13.75
0.268
215.402
13.75
1.258
11.37
13.75
8.959
215.402
14.25
0.039
13.023
14.25
0.248
225.976
14.25
1.295
13.023
14.25
8.287
225.976
14.75
0.04
14.838
14.75
0.231
236.541
14.75
1.328
14.838
14.75
7.728
236.541
15.25
0.041
16.825
15.25
0.21
246.802
15.25
1.359
16.825
15.25
7.022
246.802
15.75
0.041
18.985
15.75
0.193
256.859
15.75
1.386
18.985
15.75
6.452
256.859
16.25
0.042
21.331
16.25
0.171
266.347
16.25
1.414
21.331
16.25
5.718
266.347
16.75
0.043
23.871
16.75
0.154
275.43
16.75
1.441
23.871
16.75
5.152
275.43
17.25
0.044
26.612
17.25
0.138
284.078
17.25
1.466
26.612
17.25
4.625
284.078
17.75
0.045
29.559
17.75
0.129
292.65
17.75
1.489
29.559
17.75
4.33
292.65
18.25
0.045
32.717
18.25
0.122
301.174
18.25
1.509
32.717
18.25
4.073
301.174
18.75
0.046
36.093
18.75
0.116
309.731
18.75
1.528
36.093
18.75
3.874
309.731
19.25
0.046
39.693
19.25
0.109
318.191
19.25
1.546
39.693
19.25
3.633
318.191
19.75
0.047
43.523
19.75
0.101
326.456
19.75
1.563
43.523
19.75
3.372
326.456
20.25
0.047
47.59
20.25
0.095
334.647
20.25
1.578
47.59
20.25
3.179
334.647
20.75
0.048
51.902
20.75
0.088
342.607
20.75
1.594
51.902
20.75
2.943
342.607
21.25
0.048
56.464
21.25
0.081
350.343
21.25
1.608
56.464
21.25
2.726
350.343
21.75
0.048
61.279
21.75
0.075
357.79
21.75
1.62
61.279
21.75
2.505
357.79
22.25
0.049
66.347
22.25
0.069
364.948
22.25
1.629
66.347
22.25
2.301
364.948
22.75
0.049
71.673
22.75
0.062
371.716
22.75
1.638
71.673
22.75
2.081
371.716
23.25
0.049
77.261
23.25
0.057
378.185
23.25
1.645
77.261
23.25
1.905
378.185
23.75
0.049
83.119
23.75
0.051
384.268
23.75
1.653
83.119
23.75
1.716
384.268
24.25
0.05
89.259
24.25
0.045
389.889
24.25
1.662
89.259
24.25
1.521
389.889
24.75
0.05
95.691
24.75
0.04
395.064
24.75
1.671
95.691
24.75
1.345
395.064
25.25
0.05
102.422
25.25
0.034
399.674
25.25
1.68
102.422
25.25
1.151
399.674
25.75
0.05
109.457
25.75
0.029
403.721
25.75
1.689
109.457
25.75
0.971
403.721
26.25
0.051
116.805
26.25
0.024
407.172
26.25
1.697
116.805
26.25
0.797
407.172
26.75
0.051
124.467
26.75
0.02
410.137
26.75
1.704
124.467
26.75
0.659
410.137
27.25
0.051
132.44
27.25
0.016
412.669
27.25
1.709
132.44
27.25
0.543
412.669
27.75
0.051
140.724
27.75
0.013
414.748
27.75
1.712
140.724
27.75
0.43
414.748
28.25
0.051
149.316
28.25
0.011
416.552
28.25
1.714
149.316
28.25
0.36
416.552
28.75
0.051
158.219
28.75
0.008
418.014
28.75
1.714
158.219
28.75
0.282
418.014
29.25
0.051
167.428
29.25
0.007
419.236
29.25
1.713
167.428
29.25
0.227
419.236
29.75
0.051
176.911
29.75
0.005
420.256
29.75
1.705
176.911
29.75
0.183
420.256
30.25
0.05
186.532
30.25
0.005
421.123
30.25
1.673
186.532
30.25
0.151
421.123
30.75
0.049
196.28
30.75
0.004
421.836
30.75
1.641
196.28
30.75
0.12
421.836
31.25
0.048
206.148
31.25
0.003
422.362
31.25
1.608
206.148
31.25
0.086
422.362
31.75
0.047
216.042
31.75
0.002
422.711
31.75
1.562
216.042
31.75
0.055
422.711
32.25
0.045
225.899
32.25
0.001
422.896
32.25
1.508
225.899
32.25
0.028
422.896
32.75
0.044
235.71
32.75
0
422.974
32.75
1.456
235.71
32.75
0.012
422.974
33.25
0.042
245.472
33.25
0
422.992
33.25
1.405
245.472
33.25
0.003
422.992
33.75
0.041
255.173
33.75
0
422.998
33.75
1.355
255.173
33.75
0.001
422.998
34.25
0.039
264.802
34.25
0
423
34.25
1.306
264.802
34.25
0
423
34.75
0.038
274.353
34.75
0
423
34.75
1.259
274.353
34.75
0
423
35.25
0.036
283.817
35.25
0
423
35.25
1.212
283.817
35.25
0
423
35.75
0.035
293.097
35.75
0
423
35.75
1.156
293.097
35.75
0
423
36.25
0.032
302.069
36.25
0
423
36.25
1.087
302.069
36.25
0
423
36.75
0.031
310.73
36.75
0
423
36.75
1.021
310.73
36.75
0
423
37.25
0.029
319.081
37.25
0
423
37.25
0.958
319.081
37.25
0
423
37.75
0.027
327.111
37.75
0
423
37.75
0.897
327.111
37.75
0
423
38.25
0.025
334.815
38.25
0
423
38.25
0.838
334.815
38.25
0
423
38.75
0.023
342.188
38.75
0
423
38.75
0.781
342.188
38.75
0
423
39.25
0.022
349.226
39.25
0
423
39.25
0.727
349.226
39.25
0
423
39.75
0.02
355.923
39.75
0
423
39.75
0.675
355.923
39.75
0
423
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Received on Tue Feb 23 2010 - 00:30:02 PST
