AMBER Archive (2005)

Subject: Re: AMBER: Question about "quasih"

From: Yen-Ting Lai (c54881028_at_mail.bio.ncku.edu.tw)
Date: Wed Jun 15 2005 - 14:25:57 CDT

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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