From: Thomas Brian (thomasbrianxlii_at_gmail.com)
Date: Mon Jul 09 2012 - 18:44:55 CDT
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
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