Dear Amber users,
I am trying to compute PCA-eigenvectors from an MD trajectory and would
like to visualize them.
So I do something like:
{read and rmsfit trajectory}
matrix covar name m1 .CA
analyze matrix m1 vecs vecs.out
analyze modes displ file vecs.out out displ.out
Now, if I'm not mistaken, displ.out will contain the coordinate changes
that I would like to visualize, but how do I load them into e.g. VMD? I
know the IED program from UCSD could show amber vectors, but it's fickly
to install and I wondered if there is a more recent option to do that.
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Tue May 22 2012 - 03:00:03 PDT
