AMBER Archive (2009)

Subject: RE: [AMBER] Dyndom

From: Loeffler, Hannes (STFC,DL,CSE) (
Date: Sat Aug 29 2009 - 10:18:18 CDT

> I want to ask how to get structures from principle component analysis of MD
> trajectory, and then use them to do DynDom analysis. These structures are
> the structure with the minimal projections or maximal projections for every
> modes? Is it right? If not, how we can get it.

Well that depends on what you want to compare and hope to see. You can just
compare the average structures of the two states for example or you can chose
the two most probable structures from your projections (the structures from
the minimum and the maximum are naturally of low probability).

-- Scanned by iCritical.

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