AMBER: Projecting trajectories onto normal modes

From: Harald Lanig <>
Date: Mon, 16 Apr 2007 16:50:38 +0200

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!


  Dr. Harald Lanig            Universitaet Erlangen/Nuernberg
  Computer-Chemie-Centrum     Naegelsbachstr. 25, D-91052 Erlangen
  Phone +49(0)9131-85 26525   email: lanig AT
  Fax   +49(0)9131-85 26565
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Received on Wed Apr 18 2007 - 06:07:17 PDT
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