AMBER Archive (2003)

Subject: AMBER: Question about quasih analysis

From: Lishan Yao (yaolisha_at_pilot.msu.edu)
Date: Mon Jul 28 2003 - 09:04:26 CDT

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_at_pilot.msu.edu>
MSU

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