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From: David A. Case <case.scripps.edu>

Date: Wed, 15 Jun 2005 10:43:47 -0700

On Wed, Jun 15, 2005, Yen-Ting Lai wrote:

*>
*

*> 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?
*

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.

*>
*

*> 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?
*

The quasiharmonic modes are normalized in the "usual" way for normal modes,

such that q.M.q = 1, where M is the mass matrix. The actual amplitudes

depend upon what situation you are trying to simulate. For example, if you

want the average amplitudes at a given temperature, you can use formulas

appropriate to a harmonic oscillator in the canonical ensemble; in turn you

can use either quantum or classical statistics for this. If you have some

other (initial value) conditions that you wish to simulate, you would have

to determine the initial phases and amplitudes of the modes such that the

desired initial conditions were satisfied.

*>
*

*>
*

*> 3) For a molecule with ~100 aa, does the frequency in the output generated
*

*> by quasih look reasonable?
*

The small fragment you posted looked reasonable.

....dac

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Received on Wed Jun 15 2005 - 18:53:00 PDT

Date: Wed, 15 Jun 2005 10:43:47 -0700

On Wed, Jun 15, 2005, Yen-Ting Lai wrote:

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.

The quasiharmonic modes are normalized in the "usual" way for normal modes,

such that q.M.q = 1, where M is the mass matrix. The actual amplitudes

depend upon what situation you are trying to simulate. For example, if you

want the average amplitudes at a given temperature, you can use formulas

appropriate to a harmonic oscillator in the canonical ensemble; in turn you

can use either quantum or classical statistics for this. If you have some

other (initial value) conditions that you wish to simulate, you would have

to determine the initial phases and amplitudes of the modes such that the

desired initial conditions were satisfied.

The small fragment you posted looked reasonable.

....dac

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Received on Wed Jun 15 2005 - 18:53:00 PDT

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