AMBER Archive (2005)

Subject: AMBER: Question about "quasih"

From: Yen-Ting Lai (c54881028_at_mail.bio.ncku.edu.tw)
Date: Wed Jun 15 2005 - 11:46:22 CDT

Dear Amber Users,

I recently perform the quasiharmonic analysis of a 3ns-long trajectory by using 'quasih' subrouting in Amber7. I got the output successfully but have some questions:

1) Does quasiharmonic analysis, in the same sense as normal mode analysis, generate first 6 modes for transition and rotation?
    e.g, some few lines of the output looks like:

########################################################
               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
########################################################
 If the first 6 modes represents translation and rotation, then the lowest frequency mode is mode 7. Am I right?

2) If I remember correctly, the 'quasih' program will give a "relative" amplitude for a certain mode in the file "vecs". But if I am interested in the "absolute" amplitude but not the "relative" amplitude. How can I extract the "absolute" vibrational amplitude?

3) For a molecule with ~100 aa, does the frequency in the output generated by quasih look reasonable?

Thanks in advance

Regards,
Yen

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