AMBER Archive (2007)Subject: Re: AMBER: NAB normal mode output
From: Andreas SvrcekSeiler (svrci_at_tbi.univie.ac.at)
Date: Fri May 25 2007  04:15:46 CDT
Hi,
>> 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
Andreas

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