Re: pairlist violations

From: francesco oteri (
Date: Tue Jul 10 2012 - 03:40:42 CDT

Hi Thomas,
I dont'think there is a message when such a violation happens.
To detect this problem, namd should evaluate the distance between the atom
and checking if the distance is smaller than the cutoff and the atom it is
not in the pairlist of the reference atom.

But pairlist is supposed to be used just to avoid making this calculation.


2012/7/10 Thomas Brian <>

> 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?
> 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)
> Thanks,
> Tom

Cordiali saluti, Dr.Oteri Francesco

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