AMBER: Less error

From: Urszula Uciechowska <>
Date: Fri, 25 May 2007 12:32:56 +0200

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 <>
Date: Friday, May 25, 2007 11:18 am
Subject: Re: AMBER: NAB normal mode output

> 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
> --------------------------------------------------------------------
> ---
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun May 27 2007 - 06:07:41 PDT
Custom Search