AMBER Archive (2007)

Subject: AMBER: Projecting trajectories onto normal modes

From: Harald Lanig (Harald.Lanig_at_chemie.uni-erlangen.de)
Date: Mon Apr 16 2007 - 09:50:38 CDT

Dear AMBER community,

using ptraj it is possible to project snapshots onto mass-weighted modes
obtained by the command "matrix mwcovar" by applying e.g.
"projection modes evec.dat out proj.dat beg 1 end 2"

My question is: is it also possible to write a new trajectory after the
projection, including only the movement of the projected modes? My
intention is to visualize only one explicit mode, like it is possible by
using the VMD module IED. I found nothing about this in the manual, but
hopefully I missed it.

Thank you very much for any hint!

-Harald 

-- 
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  Dr. Harald Lanig            Universitaet Erlangen/Nuernberg
  Computer-Chemie-Centrum     Naegelsbachstr. 25, D-91052 Erlangen

  Phone +49(0)9131-85 26525   email: lanig AT chemie.uni-erlangen.de
  Fax   +49(0)9131-85 26565   http://www.ccc.uni-erlangen.de/lanig
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