Re: AMBER: NAB normal mode output

From: Andreas Svrcek-Seiler <>
Date: Fri, 25 May 2007 11:15:46 +0200 (CEST)

>> I have calculated normal modes using NAB, which produces an Amber format
>> eigenvector file. I want to calculate the dot product of these
>> eigenvectors to ensure that they are orthogonal.
Sorry for answering with a question, but why do you want to check
orthogonality (gazillions of other things much less obvious could in
principle be flawed) ?

For the checking orthogonality, one might simply add some code to nmode.c,
which is quite well documented.
Since the hessian is symmetric (mass weighted or not)
its eigenvectors *must* be orthogonal (for different
eigenvalues only). Eigenvectors for degenerate
(more then one numerically equal) eigenvalues can be made
orthogonal and should be no problem anyway.

good luck
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun May 27 2007 - 06:07:38 PDT
Custom Search