AMBER Archive (2007)

Subject: Re: AMBER: NAB normal mode output

From: David A. Case (case_at_scripps.edu)
Date: Thu May 24 2007 - 23:17:04 CDT


On Thu, May 24, 2007, nadiav_at_soton.ac.uk wrote:
>
> 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.
>
> Is this possible in Ptraj?

I don't think so...you will probably have to write a small program of your
own to check this. Note that the eigenvectors should be orthogonal with
a diagonal mass matrix used as the "metric" matrix.

...good luck....dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu