Re: Constraint failure in RATTLE algorithm

From: Axel Kohlmeyer (
Date: Wed Jun 18 2014 - 13:23:05 CDT

On Wed, Jun 18, 2014 at 1:29 PM, Douglas Houston
<> wrote:
> Hi all,
> I keep encountering the following fatal error:
> ERROR: Constraint failure in RATTLE algorithm for atom 189!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Exiting prematurely; see error messages above.
> The atom itself varies. I have searched previous messages and tried the
> suggestions (smaller timestep, minimization overkill, etc.) to no avail.
> What else could I try to get my simulation to finish? I have attached my

you need to look at this from a different perspective. first you need
to find out the reason, not try to suppress it.

how reproducible is this failure? how soon does this happen after the
start of your simulation. have you visualized your simulation around
the time of the failure and seen where exactly an atom experiences
(too) large forces. you may have a problem with bad parameters, or a
bad/incomplete topology (= .psf) file. or you are very very far away
from equilibrium and may need to do multiple iterations of
minimization and relaxation. and so on and so on. there are many ways,
but no simple general solution that works always.


> .conf file so you can see my system and the simulation parameters I am
> specifying.

> cheers,
> Doug
> _____________________________________________________
> Dr. Douglas R. Houston
> Lecturer
> Institute of Structural and Molecular Biology
> Room 3.23, Michael Swann Building
> King's Buildings
> University of Edinburgh
> Edinburgh, EH9 3JR, UK
> Tel. 0131 650 7358
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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