From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
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).
Giacomo
On Fri, Jul 21, 2017 at 1:06 PM, Francesco Pietra <chiendarret_at_gmail.com>
wrote:
> 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 http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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