Dear Mr. Case,
Thanks for your helpful reply. In order to make myself more clear, I need to
ask one more question.(please don't mind)
>>
>> 1) Does quasiharmonic analysis, in the same sense as normal mode
>> analysis,
>> generate first 6 modes for transition and rotation?
>
> Before running quasih, you need do an rms fit to superimpose your
> structures
> to some reference structure. This procedure removes translations and
> rotations, so they will not show up in the quasiharmonic analysis.
>
I did perform rms fit over the whole trajectory before I ran quasih. Does
this mean that the lowest frequency in my case is mode 1 instead of mode 7?
########################################################
freq. E Cv S
cm**-1 kcal/mol cal/mol-kelvin cal/mol-kelvin
--------------------------------------------------------------------------------
Total 31.388 105.226 507.264
translational 0.888 2.979 53.529
rotational 0.888 2.979 52.929
vibrational 29.612 99.268 400.806
1 2.445 0.592 1.986 10.801
2 2.658 0.592 1.986 10.635
3 3.708 0.592 1.986 9.974
4 4.442 0.592 1.986 9.616
5 4.734 0.592 1.986 9.489
6 5.632 0.592 1.986 9.144
7 5.706 0.592 1.986 9.118
8 6.225 0.592 1.986 8.946
9 6.759 0.592 1.986 8.782
10 7.033 0.592 1.986 8.703
########################################################
Thanks again
Regards,
Yen
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Received on Wed Jun 15 2005 - 20:53:01 PDT
