AMBER Archive (2004)

Subject: AMBER: rms fluct and displacement in modes analysis

From: Vlad Cojocaru (
Date: Tue Oct 12 2004 - 05:47:34 CDT

Dear Amber users,
   Could somebody indicate me the way the rms fluct and displacements
are calculated during mode analysis in ptraj? What do these values
represent actualy?
   Second, why the rms fluct is calculated along X, Y, Z axes but also a
general rms is calculated while for the displacement only the displ.
along X, Y, and Z is given?
   I am currently dooing some PCA and I would like to fully understand
what's behind ptraj commands.
   A short explanation or reference would be welcomed.
Thank you very much in advance
vlad cojocaru

Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
home tel: ++49-551-9963204  

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