<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div><div>Vitaly,</div><div><br></div><div>your are right in principle but for "real" systems long-range LJ </div><div>interactions do matter a lot. </div><div><br></div><div>In addition Justin reference the following is a good example of</div><div>the effect of treatment of long-range interaction:</div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 9.5px/normal Helvetica; "><i><span class="Apple-style-span" style="font-size: 11px; font-style: normal; "><b>Ane</b><b>zo et al. </b></span>J. Phys. Chem. B </i><b>2003, </b><i>107, </i>9424<span style="font: 9.5px Times"><i>-</i></span>9433</div></div><div><br></div><div>XAvier.</div><div><br></div><div><div>On Mar 25, 2010, at 11:46 AM, Vitaly V. Chaban wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>XAvier,<br><br>You should probably know that E(LJ)(r)->0 at r->2.5*sigma. This is a<br>result of pure mathematical analysis. If all the sigmas in your system<br>are less than 0.4 nm, then after r=1.0 nm, the energy is very close to<br>zero.<br><br>All your below statement are correct but they do not address the<br>problem if E(LJ)->0 at R(cutoff). This was the only hint I posted<br>before.<br><br>Vitaly<br><br>On Thu, Mar 25, 2010 at 12:37 PM, XAvier Periole <<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>> wrote:<br><blockquote type="cite"><br></blockquote><blockquote type="cite">the development of biomolecular force fields in general have tough<br></blockquote><blockquote type="cite">the community that cutoff values are important parameters for any<br></blockquote><blockquote type="cite">force field, this is true for both Elec and vdW interactions.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">The example of a bilayer was the most obvious to me when thinking<br></blockquote><blockquote type="cite">of the effect of the vdW cutoff. The balance between the Elec and vdW<br></blockquote><blockquote type="cite">is determinant to the properties of the bilayer. No particular atom-pair<br></blockquote><blockquote type="cite">in mind, though.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">It important not to give the wrong impression to people new in the<br></blockquote><blockquote type="cite">field. The literature is full of reports of cutoff artefacts ...<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On Mar 25, 2010, at 9:29 AM, Vitaly V. Chaban wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">On Thu, Mar 25, 2010 at 12:45 AM, XAvier Periole <<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>> wrote:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">On Mar 24, 2010, at 10:58 PM, Vitaly V. Chaban wrote:<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Hi,<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I want to test different values of cutoff for vdw. However, in the list<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">someone said cutoff = 0.9 for vdw was used for paramaterizing of<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Gromos<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">force field, other values would cause error, and also there was someone<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">saying that cutoff for vdw should be set to 1.4. Can >someone make this<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">question clear? Thanks a lot.<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">The common rule for all FFs is to set the LJ-cutoff around<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">2.5*sigma(LJ12-6). In fact, you'll get about 0.9 nm for the most<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">objects. I see nothing terrible if you use, say, 1.4 nm just because<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">the difference will be negligible.<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Where is that coming from? This is so wrong!<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">From the properties of LJ12-6 curve.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Just test it. :)<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I've you ever tried that on a lipid bilayer?<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">My interests are a bit shifted from bilayers. What concrete atom pair<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">will cause the problem in your example?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Who could ever say (whatever force field) a vdW cutoff of 0.9/1.4 nm<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">is no difference?<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">--<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Dr. Vitaly Chaban<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">--<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><br><br><br>-- <br>Dr. Vitaly Chaban<br><a href="http://chaban.at.ua">http://chaban.at.ua</a><br></div></blockquote></div><br></body></html>