AMBER Archive (2002)

Subject: drifting from average structure

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Dear Amber users,
   Thanks a lot for the answers regarding the averaging problems that I
had during past days.
   Now I want to calculate the drift of my molecule during the dynamics
from the average structure. I would like an advice. How do you do it
usually. First applying energy minimization to the average structure and
then fitting the trajectory to the minimized structure or use the row
average structure for fitting?
  Thanks a lot again. Hope that I am not asking too trivial questions!
Best wishes,
vlad

-- 
Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1389 
e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
home tel: ++49-551-9963204  

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