<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>On Apr 12, 2009, at 1:17 PM, David van der Spoel wrote:</div><blockquote type="cite"><div><font class="Apple-style-span" color="#000000"><br></font>Why is there a need for a special neighbor list? Why not use the normal one (possibly without exclusions)</div></blockquote><br></div><div>Because doing that too early without extensive is a guaranteed way to introduce stupid bugs. Just a few examples:</div><div> </div><div>1. It is a pain to debug GB when the particles are in three separate neigborlists (LJ-only, Coul-only, both)</div><div>2. If you use twin-range cutoffs you will get problems when LJ-only atoms are not included in the long-range neighborlist, but they should still be included for calculating born radii.</div><div>3. There is no "normal neighborlist without exclusions" - the neighborlist does not include excluded atoms. You would end up writing two copies of every single routine you need, one processing neighborlists, and one processing entries from the exclusion list.</div><div>4. Long-term, there is no specific reason why rgb should be the same as the interaction cutoff</div><div><br></div><div><br></div><div>Cheers,</div><div><br></div><div>Erik</div></body></html>