it is in the src/addles directory but it is called SIZE.h not SIZE.BLOCK.
On 5/25/07, Urszula Uciechowska <urszula.uciechowska.pharmazie.uni-halle.de>
wrote:
>
>
> 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.tbi.univie.ac.at>
> Date: Friday, May 25, 2007 11:18 am
> Subject: Re: AMBER: NAB normal mode output
> To: amber.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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Received on Sun May 27 2007 - 06:07:41 PDT
