From chemistry-request@ccl.net Tue Mar 10 12:15:47 1992
Date: Tue, 10 Mar 92 07:22:19 -0800
From: pak@cgl.ucsf.EDU (Peter Kollman)
Subject: non-bonded cutoffs
To: chemistry@ccl.net
Status: R

I wanted to add to the non-bond cutoff debate.  Even though one typically
uses a non-bonded cutoff that is too small, e.g. 8 angstoms, in many
macromolecular simulations, it is likely better to use ewald summation than
no cutoff in crystal simulations..(what does infinite cutoff really mean 
when one has periodic boundary conditions..it is really undefined until you
define your unit cell, which you can make larger and larger)...even in
solution simulations without periodic boundary conditions, with many
formal charges, I would argue that infinite cutoffs might lead to
artifacts because one can't run the simulations long enough to get appropriate
averaging of all these formal charges to give realistic ion atmosphere
effects...the cure may be worse than the disease...i do think longer than
8 angstrom cutoffs are appropriate and recommend dual cutoffs(c.f. Berendsen,
van Gunsteren,Darden,Charifson) which can consider effects out to, e.g. 15
to 20 angstroms at little computational overhead...but in summary, there are
many things more important in reducing simulation artefacts than switching
to an infinite non-bonded cutoff--even if we could, i don't think we should.