From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Nov 17 2021 - 10:27:39 CST
This message is the key:
colvars: This is usually the result of an ill-defined set of atoms for
rotational alignment (RMSD, rotateReference, etc).
If the structure of the group of atoms changes too much, it becomes
possible that a pure rotation is not the transformation that minimizes the
RMSD, but another transformation does (e.g. rotation + reflection across a
You do not need to change the time step, but instead pick a selection that
is guaranteed to have only moderate changes in structure. Practically
speaking, the RMSD should remain much lower than the radius of gyration.
If you compute that RMSD in VMD you will have a similar problem, just with
a different outcome because the numerical algorithm is different.
On Wed, Nov 17, 2021 at 11:03 AM Ashutosh Shandilya <scfbioiitd_at_gmail.com>
> I am running ABF and getting this error.
> Frame index: 32 ; optimal RMSD = 4.87456
> Frame index: 31 ; optimal RMSD = 4.87456
> Frame index: 30 ; optimal RMSD = 4.87456
> Frame index: 29 ; optimal RMSD = 4.87456
> Frame index: 28 ; optimal RMSD = 4.87456
> colvars: Prepared sample and gradient buffers at step 0.
> colvars: Too many iterations in routine jacobi.
> colvars: This is usually the result of an ill-defined set of atoms for
> rotational alignment (RMSD, rotateReference, etc).
> colvars: Too many PFATAL ERROR: Error in the collective variables module
> (see above for details)
> FATAL ERROR: Error in the collective variables module (see above for
> I have used different timesteps but still I am getting this error. Any
> Many thanks
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