AMBER Archive (2007)

Subject: AMBER: Less error

From: Urszula Uciechowska (urszula.uciechowska_at_pharmazie.uni-halle.de)
Date: Fri May 25 2007 - 05:32:56 CDT

Dera AMber useres,

I try to use LES simulation for a part of a protein and get following error in the output after
started addles. change SIZE.BLOCK and recomplie, I know that my system is to large than the
default limits and I need to increased some value. My question is where I can find this file or
where should it be?

Thanks in advance

Best Regards,
Urszula Uciechowska

MSc.PhD Student
Medicinal Chemistry Group
University of Halle-Wittenberg

----- Original Message -----
From: Andreas Svrcek-Seiler <svrci_at_tbi.univie.ac.at>
Date: Friday, May 25, 2007 11:18 am
Subject: Re: AMBER: NAB normal mode output
To: amber_at_scripps.edu

> 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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