AMBER Archive (2007)

Subject: Re: AMBER: High Standard Deviation for nmode (TSVIB) mm_pbsa

From: David A. Case (case_at_scripps.edu)
Date: Sat Feb 17 2007 - 15:22:38 CST

On Sat, Feb 17, 2007, Rima Chaudhuri wrote:

> I looked at the structure in vmd and nothing looks weird
> post-simulation, hence I doubt if there is an outlier.

I think you need to look at the nmode outputs themselves, study the
distribution of low-frequency eigenvalues, and see if you can spot anything.
Not knowing anything about your system, I can't say from my vantage point
what might be happening. Of course, what you see could be real, as well.

...dac

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