Thanks Dave,
Yes, I did superimpose (I provided a sample input for ptraj in my
previous email).
I will try to play around with some toy system before going back to my
systems ... I just thought maybe somebody has seen such a behavior
before and could give some hints on where the problem might be ...
Best wishes
Vlad
Just in case it might help .... Here is a more detailed chunk of the output
*******************
- Thermochemistry -
*******************
temperature 298.150 kelvin
pressure 1.00000 atm
molecular mass (principal isotopes) 50699.61600 amu
principal moments of inertia (nuclei only) in amu-A**2:
13071316.84 33416392.14 37720238.26
rotational symmetry number 1.
Warning-- assumption of classical behavior for rotation
may cause significant error
rotational temperatures (kelvin) 0.00000 0.00000 0.00000
zero point vibrational energy -574104810.9 (joules/mol)
************ (kcal/mol)
-218.6606748 (hartree/particle)
Warning-- *** vibrations have low frequencies and may represent hindered
internal rotations. The contributions printed below assume
that these
really are vibrations.
warning: setting vibrational entropy to zero for mode 13530
with vtemp = -255030915.01682976
warning: setting vibrational entropy to zero for mode 13531
with vtemp = -136638356.27652273
warning: setting vibrational entropy to zero for mode 13532
with vtemp = -97969224.467119500
....... (continues with the same warnings ...) ...............
warning: setting vibrational entropy to zero for mode 19059
with vtemp = -117200.85428099972
freq. E Cv S
cm**-1 kcal/mol cal/mol-kelvin cal/mol-kelvin
--------------------------------------------------------------------------------
Total *********** NaN 20143.554
translational 0.888 2.979 58.245
rotational 0.888 2.979 62.384
vibrational *********** NaN 20022.926
1 0.208 0.592 1.986 15.699
2 0.277 0.592 1.986 15.129
3 0.345 0.592 1.986 14.689
4 0.397 0.592 1.986 14.413
5 0.661 0.592 1.986 13.399
6 0.713 0.592 1.986 13.249
7 0.838 0.592 1.986 12.929
8 0.923 0.592 1.986 12.736
9 1.034 0.592 1.986 12.510
10 1.183 0.592 1.986 12.243
11 1.235 0.592 1.986 12.157
12 1.340 0.592 1.986 11.996
13 1.420 0.592 1.986 11.881
14 1.496 0.592 1.986 11.777
15 1.552 0.592 1.986 11.704
16 1.636 0.592 1.986 11.600
17 1.728 0.592 1.986 11.491
18 1.773 0.592 1.986 11.439
19 1.817 0.592 1.986 11.391
20 1.885 0.592 1.986 11.318
21 1.975 0.592 1.986 11.226
22 2.043 0.592 1.986 11.158
23 2.116 0.592 1.986 11.088
24 2.243 0.592 1.986 10.972
25 2.277 0.592 1.986 10.943
26 2.402 0.592 1.986 10.837
27 2.445 0.592 1.986 10.801
28 2.508 0.592 1.986 10.751
29 2.633 0.592 1.986 10.654
30 2.767 0.592 1.986 10.556
31 2.810 0.592 1.986 10.525
32 2.864 0.592 1.986 10.487
33 2.945 0.592 1.986 10.432
34 2.982 0.592 1.986 10.407
35 3.088 0.592 1.986 10.338
36 3.135 0.592 1.986 10.308
37 3.174 0.592 1.986 10.283
38 3.217 0.592 1.986 10.256
39 3.286 0.592 1.986 10.214
40 3.378 0.592 1.986 10.159
41 3.430 0.592 1.986 10.129
42 3.435 0.592 1.986 10.126
43 3.456 0.592 1.986 10.114
44 3.577 0.592 1.986 10.046
45 3.606 0.592 1.986 10.030
46 3.656 0.592 1.986 10.002
47 3.722 0.592 1.986 9.967
48 3.773 0.592 1.986 9.940
49 3.820 0.592 1.986 9.915
50 3.834 0.592 1.986 9.908
51 3.946 0.592 1.986 9.851
52 3.976 0.592 1.986 9.836
53 4.076 0.592 1.986 9.786
54 4.125 0.592 1.986 9.763
55 4.191 0.592 1.986 9.731
56 4.212 0.592 1.986 9.721
57 4.262 0.592 1.986 9.698
58 4.302 0.592 1.986 9.679
59 4.350 0.592 1.986 9.657
60 4.435 0.592 1.986 9.619
61 4.447 0.592 1.986 9.613
62 4.498 0.592 1.986 9.591
63 4.565 0.592 1.986 9.562
64 4.609 0.592 1.986 9.542
65 4.696 0.592 1.986 9.505
66 4.763 0.592 1.986 9.477
67 4.810 0.592 1.986 9.458
68 4.814 0.592 1.986 9.456
69 4.905 0.592 1.986 9.419
70 4.927 0.592 1.986 9.410
71 4.977 0.592 1.986 9.390
72 5.023 0.592 1.986 9.371
73 5.041 0.592 1.986 9.364
74 5.113 0.592 1.986 9.336
75 5.120 0.592 1.986 9.333
76 5.182 0.592 1.986 9.310
77 5.203 0.592 1.986 9.302
78 5.282 0.592 1.986 9.272
79 5.305 0.592 1.986 9.263
80 5.343 0.592 1.986 9.249
81 5.357 0.592 1.986 9.244
82 5.451 0.592 1.986 9.209
83 5.514 0.592 1.986 9.186
84 5.578 0.592 1.986 9.163
85 5.611 0.592 1.986 9.152
86 5.629 0.592 1.986 9.145
87 5.686 0.592 1.986 9.125
88 5.748 0.592 1.986 9.104
89 5.770 0.592 1.986 9.096
90 5.828 0.592 1.986 9.076
91 5.876 0.592 1.986 9.060
92 5.892 0.592 1.986 9.055
93 5.957 0.592 1.986 9.033
94 5.972 0.592 1.986 9.028
95 6.016 0.592 1.986 9.013
96 6.039 0.592 1.986 9.006
97 6.102 0.592 1.986 8.985
98 6.184 0.592 1.986 8.958
99 6.200 0.592 1.986 8.954
100 6.253 0.592 1.986 8.936
.................. (continues like this .. until ...) ............
7997 1358.099 1.947 0.121 0.021
7998 1362.292 1.953 0.120 0.021
7999 1366.865 1.959 0.118 0.021
8000 1372.397 1.967 0.116 0.020
8001 83395.518 119.227 0.000 0.000
8002541164.588 773.681 NaN 0.000
8003552609.416 790.043 NaN 0.000
8004553227.656 790.927 NaN 0.000
8005555544.100 794.239 NaN 0.000
8006557572.554 797.139 NaN 0.000
8007558879.512 799.007 NaN 0.000
8008560231.050 800.939 NaN 0.000
8009562143.724 803.674 NaN 0.000
8010563281.075 805.300 NaN 0.000
8011564392.364 806.889 NaN 0.000
8012567215.524 810.925 NaN 0.000
8013568793.379 813.181 NaN 0.000
8014569109.740 813.633 NaN 0.000
8015571332.940 816.811 NaN 0.000
8016572492.789 818.470 NaN 0.000
.................. (continues like this .. until ...) ............
13526********** 67467.092 NaN 0.000
13527********** 89906.420 NaN 0.000
13528********** 120303.585 NaN 0.000
13529********** 179745.375 NaN 0.000
13530********** 253229.659 0.000 0.000
13531********** 135673.294 0.000 0.000
13532********** 97277.278 0.000 0.000
13533********** 83261.582 0.000 0.000
13534********** 71441.825 0.000 0.000
13535********** 65483.927 0.000 0.000
.................. (continues like this .. until ...) ............
19055********** 791.335 0.000 0.000
19056********** 789.431 0.000 0.000
19057********** 786.797 0.000 0.000
19058********** 777.133 0.000 0.000
19059-81399.181 116.373 0.000 0.000
On 10/29/2013 12:45 PM, David A Case wrote:
> On Tue, Oct 29, 2013, Vlad Cojocaru wrote:
>> I did an entropy estimation from a quasi harmonic analysis in ptraj of a
>> 150 ns simulation (50.000 frames). I get huge numbers for the
>> vibrational entropy (sample output below).
>>
>> -------------- sample output complex---------------------------
>> freq. E Cv S
>> cm**-1 kcal/mol cal/mol-kelvin cal/mol-kelvin
>> --------------------------------------------------------------------------------
>> Total *********** NaN 20143.554
>> translational 0.888 2.979 58.245
>> rotational 0.888 2.979 62.384
>> vibrational *********** NaN 20022.926
> That fact that you have all "***" and "NaN" (not a number) in your output
> certainly suggests that something is wrong. I don't see how this can easily
> be debugged remotely: look for information about the individual frequencies.
> Did you superimpose your trajectory (to remove overall rotation and
> translation) before running the quasiharmonic analysis? You may want to gain
> experience on a simpler, smaller system to make sure you are confident in how
> everything is supposed to work.
>
> ...dac
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
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Received on Tue Oct 29 2013 - 06:00:03 PDT
