Re: AMBER: Projecting trajectories onto normal modes

From: M. L. Dodson <>
Date: Mon, 16 Apr 2007 10:41:50 -0500

On Monday 16 April 2007 09:50, Harald Lanig wrote:
> 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

Not exactly what you requested, but I have a nab program
( which writes a
variant of the pdb format corresponding to the "pqr" option,
putting one eigenvector into the coordinate fields and the
Euclidean length of the corresponding displacement into the
"charge" field. You might be able to use a similar approach to
generate what you want. Let me know if you want the code.

Bud Dodson
M. L. Dodson
Email:	mldodson-at-houston-dot-rr-dot-com
Phone:	eight_three_two-five_63-386_one
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Received on Wed Apr 18 2007 - 06:07:18 PDT
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