Re: Can a small langevinDamping coefficient lead to 'ERROR: atoms moving too fast'?

From: Gianluca Interlandi (
Date: Mon Aug 26 2013 - 11:56:47 CDT

> A few of the simulations aborted with the following message:
> "ERROR: Atoms moving too fast; simulation has become unstable."
> Could a small damping coefficient lead to such errors? If so, what would be the scenario
> giving rise to some atom moving too fast?

Atoms move too fast if there are huge forces which is often the result of
an incorrect system setup, like atoms clashing or too close too each
other. You need to perform sufficient minimization and equilibration
before starting production. You might want to inspect your initial PDB for
clashing atoms. Sometimes hydrogen atoms clash after they have been built.
In this case, perform minimization and equilibration with harmonic
constraints on heavy atoms in order to minimize and equilibrate the
hydrogen atoms.


Gianluca Interlandi, PhD

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.

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