From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Wed Jun 18 2014 - 20:29:08 CDT
This may or may not be the source of your problem, but I notice you’re using CHARMM-36 parameters. One key difference between CHARMM-36 and the CHARMM-27 files distributed with NAMD is that it doesn’t explicitly define angles and dihedrals in its patches. In practice what this means is that if you forget to include a “regenerate angles dihedrals” line at the end of your psfgen script (or check “Regenerate angles/dihedrals” under the Options menu in AutoPSF) then any patched residues will begin moving without any angular or torsional restraints, which of course leads to all sorts of strange behaviour.
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of Aron Broom
Sent: Thursday, 19 June 2014 5:07 AM
To: Axel Kohlmeyer
Cc: Douglas Houston; Namd Mailing List
Subject: Re: namd-l: Constraint failure in RATTLE algorithm
to second Axel, you need to pin down what in your system is not setup properly.
Often if something is incredibly wrong the failure will be so rapid that from one frame to the next you'll go from nice structure to total garbage. You should then, decrease the timestep far enough that you actually can get an intermediate frame, that is, one where the potential energy has shot up from the starting coordinates, but where the simulation has not yet crashed. You might have to go very low for this, like hundredths of a fs.
Also, you should set the temperature to 0 and turn off any barostat, just to reduce any noise that might make visualization harder. What you want to see when you view the trajectory, is 99% of your atoms being completely motionless, while one part is moving around and hitting other things.
Just because the atom numbers that cause the crash are changing doesn't mean the source isn't consistent, it could just be that whatever atoms your messed up region smashes into after going hay-wire are different.
On Wed, Jun 18, 2014 at 2:23 PM, Axel Kohlmeyer <akohlmey_at_gmail.com<mailto:akohlmey_at_gmail.com>> wrote:
On Wed, Jun 18, 2014 at 1:29 PM, Douglas Houston
> 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
> Dr. Douglas R. Houston
> 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 akohlmey_at_gmail.com<mailto:akohlmey_at_gmail.com> http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.
Aron Broom M.Sc
Department of Chemistry
University of Waterloo
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