Re: nonequilibrium SMD with fixed atoms

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Jan 24 2018 - 10:11:18 CST

Hi Katja, the error:
colvars: Too many iterations in routine jacobi.

is given by the function that computes the rotational alignment/fitting
onto a reference structure. It's very likely that one the RMSD restraints
in the colvars.conf file included in the tutorial is losing its structure.

Try looking at the trajectory in VMD and see what's going on. You may have
to make DCDfreq smaller to have the output written frequently.

Giacomo

On Wed, Jan 24, 2018 at 10:27 AM, Ekaterina Sobakinskaja <
Ekaterina.Sobakinskaja_at_jku.at> wrote:

> Dear NAMD users,
>
> in my simulations I need to rotate 2 helices in the protein complex to
> obtain conformation I need. Other helices must remain in their places.
>
> I'm going to use nonequlibrium SMD protocol. I was trying the example
> GlPt, given in the Tutorial, and fixed few helices in the protein, using
>
> fixedAtoms on
> fixedAtomsFile fixed_atoms.ref
> fixedAtomsCol B
>
> I have also modified colvars.conf accordingly.
>
> The simulations were started, but then I got the error message:
>
> Reason: FATAL ERROR: Error in the collective variables module: exiting.
> colvars: Too many iterations in routine jacobi.
> FATAL ERROR: Error in the collective variables module: exiting.
>
> How can I resolve it? Or may be I should use another method to solve my
> problem?
>
> Any help will be appreciated!
>
> thank you in advance,
>
> Katja
>
>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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