Re: Too many iterations in routine jacobi.

From: Giacomo Fiorin (
Date: Fri Jul 21 2017 - 12:49:56 CDT

Hi Francesco, this is an error that occurs in the RMSD fitting -
orientational alignment routine. If the number of atoms involved is too
few (which ones?), or in general if you come into an issue with
linearly-dependent vectors in the associated matrix, the error comes out.

Ideally, you want more than 4 atoms for an orientational fit, and a
flexible structure but not one that changes too much internally (i.e.
protein unfolding would also raise an error).


On Fri, Jul 21, 2017 at 1:06 PM, Francesco Pietra <>

> Hello:
> While running a FEP simulation, RATTLE ts=2.0fs, error at initial stages:
> colvars: Too many iterations in routine jacobi.
>> colvars: No such file or directory
>> FATAL ERROR: Error in the collective variables module: No such file or
>> directory
> In contrast, no errors with "rigid bonds water" ts=1.0fs, hence I do not
> understand which mismatch is alluded to.
> Thanks
> for advice
> francesco pietra

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD

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