<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><DIV>Greetings,</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>A summary of different energy contributions is written to the the md.log file during an MD calculation. Below is an extract,...</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV> Energies (kJ/mol)</DIV><DIV> Angle Ryckaert-Bell. LJ-14 Coulomb-14 LJ (SR)</DIV><DIV> 2.93814e+03 4.04053e+01 7.73620e+01 -2.06722e+03 -1.30833e+04</DIV><DIV> Coulomb (SR) Position Rest. Potential Kinetic En. Total Energy</DIV><DIV> 1.08433e+03 1.74709e+01 -1.09928e+04 7.09543e+03 -3.89738e+03</DIV><DIV> Temperature Pressure (bar)</DIV><DIV> 3.03856e+02 8.52321e+02</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>The Potential energy is simply the sum of Angle, Ryckaert-Bell, LJ-14, Coulomb(14), LJ(SR), Coulomb(SR) and Position Rest. energies.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>I have two questions,...</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>1) What does the acronym 'SR' stand for?</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>2) Why is there no Bond term in the potential energy?</DIV><DIV><BR class="khtml-block-placeholder"></DIV>Regards,<DIV><BR class="khtml-block-placeholder"></DIV><DIV>Brian.</DIV><DIV><BR><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">Dr Brian J Smith</FONT></P><P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">The Walter & Eliza Hall Institute of Medical Research</FONT></P><P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">1G Royal Parade, Parkville, Victoria 3050, Australia</FONT></P><P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">Ph: +61 (0)3 9345 2687 Fax: +61 (0)3 9345 2686</FONT></P><P style="margin: 0.0px 0.0px 0.0px 0.0px"><A href="http://www.wehi.edu.au/brian_smith">http://www.wehi.edu.au/brian_smith</A></P><BR class="Apple-interchange-newline"></SPAN> </DIV><BR></DIV></BODY></HTML>