Hi:
I use quasih program to do the entropy calculation for
6-hydroxymethyl-7,8-dihydropterin. After about 1ns MD simulation, the
entropy converges. This is the result I get:
freq. E Cv S
cm**-1 kcal/mol cal/mol-kelvin cal/mol-kelvin
--------------------------------------------------------------------------------
Total 22.164 72.625 265.174
translational 0.888 2.979 41.682
rotational 0.888 2.979 33.787
vibrational 20.388 66.667 189.705
1 0.960 0.592 1.986 12.657
2 0.995 0.592 1.986 12.586
3 1.015 0.592 1.986 12.547
4 1.128 0.592 1.986 12.337
5 1.599 0.592 1.986 11.645
6 2.884 0.592 1.986 10.473
7 4.662 0.592 1.986 9.519
8 30.277 0.593 1.982 5.806
9 36.189 0.594 1.981 5.452
10 38.096 0.594 1.980 5.351
11 44.140 0.594 1.978 5.059
12 46.443 0.595 1.978 4.959
13 49.671 0.595 1.976 4.826
14 51.328 0.595 1.976 4.761
15 56.856 0.596 1.973 4.559
16 58.513 0.596 1.973 4.502
17 63.585 0.597 1.970 4.338
18 64.496 0.597 1.970 4.310
19 68.834 0.598 1.968 4.182
20 72.462 0.598 1.966 4.081
21 78.853 0.599 1.962 3.915
22 79.971 0.599 1.961 3.888
23 86.409 0.601 1.957 3.736
24 88.983 0.601 1.956 3.678
25 93.060 0.602 1.953 3.591
26 100.987 0.604 1.947 3.431
27 105.429 0.605 1.944 3.348
28 119.333 0.608 1.932 3.108
29 122.289 0.609 1.929 3.060
30 125.331 0.610 1.926 3.013
31 131.047 0.612 1.921 2.927
32 139.960 0.614 1.912 2.801
33 151.001 0.618 1.900 2.656
34 155.558 0.620 1.895 2.600
My questions are:
1, Those low frequencies are kind of too low. what kind of motion can
have these low frequencies for a small organic molecule. When I use MP2
to do the frequency analysis, I get totally different results.
2. The number of frequencies given by this program is less than or equal
to 3N/2 (Is there any reason behind this?).
3. How the moments of inertia are calculated, from the average structure
or from each structure then take an average?
4. When I just use the heavy atoms to do the same thing. I lose not only
high frequencies but also low frequencies. Any explanation? It seems
that I should only lose high frequencies.
Thanks in advance.
Sincerely
Lishan
--
Lishan Yao <yaolisha.pilot.msu.edu>
MSU
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Received on Mon Jul 28 2003 - 15:53:01 PDT
