AMBER Archive (2004)

Subject: AMBER: modes analysis in ptraj

From: Vlad Cojocaru (
Date: Thu Oct 14 2004 - 07:13:14 CDT

Dear Amber users,
   I am performing PCA using ptraj from Amber8. Some days ago I sent the
email below to the list. Excuse me if I insisit on this but I would
really appreciate to receive at least a reference where I can read the
answers to my questions. Here is the email that I sent:

"Dear Amber users,
  Could somebody indicate me the way the rms fluct and displacements are
calculated during modes 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.

When I mean mode analysis I reffer to the following commands

matrix covar name covarmat @CA
analyze matrix covarmat out evecs.pev vecs 25
analyze modes displ[fluct] out displ-CA.dat file evecs.pev beg 1 end 6

I meant the rms fluct and the displacement calculated using the last
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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