Re: Periodic cell has become too small

From: Axel Kohlmeyer (
Date: Thu Dec 24 2009 - 04:31:11 CST

> Then I tried to equilibrate the system, with same restraints, holding
> the 310K temperature, disabling useFlexibleCell ad setting "margin 5".
> After new 1000 steps of minimization, the run crashed with:
> Periodic cell has become too small.
> Any suggestion how to make the equilibration smoother (I guess that
> there are too sudden changes) from users that came across a similar
> problem would be welcome.

the advice is the same that has been given
too numerous other people on this before.
just do a restart.

the problem is that NAMD does not support building
a complete new so-called patch grid during a run.
this is a deliberate choice as this would require a
lot of effort for something that is not important during
production, can be easily circumvented, and takes
part during a phase of setting up a system, where
manual intervention is required regardless.

> francesco pietra

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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