<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi,<DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR><DIV><DIV>On Oct 12, 2005, at 10:45 PM, David wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">On Wed, 2005-10-12 at 22:18 +0200, Erik Lindahl wrote:</DIV> <BR><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">A bug indeed. Fixed in both branches of CVS, and will be in a 3.3.1 <SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">update in your near future.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">In the meantime, you can download an updated src/kernel/toppush.c from</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="ftp://ftp.gromacs.org/pub/tmp/toppush.c">ftp://ftp.gromacs.org/pub/tmp/toppush.c</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV> <BR></BLOCKQUOTE><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">It's probably good to note that this is a bug in grompp rather than</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">mdrun and that it can be prevented (using manual labor) by writing the</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Ryckaert-Bellemans parameters twice for each dihedral (such that A and B</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">state are identical).</DIV></BLOCKQUOTE></DIV><FONT class="Apple-style-span" color="#0000DD"><BR class="khtml-block-placeholder"></FONT></DIV><DIV><FONT class="Apple-style-span" color="#0000DD">Definitely - and you only need to do it for the handful of dihedrals where the parameters are specified explicitly in the dihedrals topology section, e.g. with a define string.</FONT></DIV><DIV><FONT class="Apple-style-span" color="#0000DD"><BR class="khtml-block-placeholder"></FONT></DIV><DIV><FONT class="Apple-style-span" color="#0000DD">Cheers,</FONT></DIV><DIV><FONT class="Apple-style-span" color="#0000DD"><BR class="khtml-block-placeholder"></FONT></DIV><DIV><FONT class="Apple-style-span" color="#0000DD">Erik</FONT></DIV><DIV><FONT class="Apple-style-span" color="#0000DD"><BR class="khtml-block-placeholder"></FONT></DIV><DIV><FONT class="Apple-style-span" color="#0000DD"><BR class="khtml-block-placeholder"></FONT></DIV></BODY></HTML>