AMBER Archive (2007)

Subject: Re: AMBER: ptraj and quasi harmonic analysis

From: Hans Lee (indyhans2000_at_yahoo.com)
Date: Fri Apr 20 2007 - 11:35:49 CDT

David,
   
  The description I provided below was in response to Chris's comments about normal mode analysis. Quasi harmonic analysis has been carried out on a 3ns trajectory of 3000 frames without minization. The results from normal mode analysis and from quasi harmonic is not comparable. Tom has brought up his point of fitting each region before performing the quasi harmonic analysis. Certainly I will try that.
   
  -Hans

"David A. Case" <case_at_scripps.edu> wrote:
  On Thu, Apr 19, 2007, Hans Lee wrote:
>
>
> Yes. I have 200 frames for complex, receptor and ligand respectively.
> Instead of running separate trajectories, simulation was carried out on
> the complex only. Snapshots for receptor and ligand were extracted from
> the complex trajectories. I am not sure how the results will improve if
> simulations were carried out on complex, receptor and ligand respectively.
> The structures were minimized before Matrix calculation.

First, 200 snapshots is way too few to see much of anything from quasiharmonic
analysis, and enormously too few to use to compute an entropy. Second, the
structures should not ordinarily be minimized prior to quasiharmonic analysis:
the idea is to help in understanding the nature of the thermal fluctuations
that take place.

...hope this helps...dac

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