Re: pairlist violations

From: Axel Kohlmeyer (
Date: Tue Jul 10 2012 - 05:24:01 CDT

On Tue, Jul 10, 2012 at 1:44 AM, Thomas Brian <> wrote:
> Hi namd-l,
> If an atom enters another atoms cutoff without being in its pairlist, what
> error/warning, if any is displayed in the output file?

no. such a test would *kill* performance.
it is up to the user, to choose reasonable
settings, so that this does not happen.

> Also, does namd back up and redo the last "cycle" number of timesteps? (I


> saw somewhere that pairlist violations do not affect the dynamics and I
> don't know how that would be possible unless namd backed up and redid
> calculations)

well, if you are missing interactions due to too infrequent pairlist rebuilds
to too small a cutoff for it, then you *do* miss those interactions. if this is
infrequent, however, you may not notice. whether this is a good or bad
thing, is a different discussion.


> Thanks,
> Tom

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

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