<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><DIV><FONT class="Apple-style-span" color="#0000DD">Hi,</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></FONT><BLOCKQUOTE type="cite"> -------------------------------------------------------<BR> <BR> I used other Protein and the same happens, but in a different residue. Both have in common being a Proline residue. I am not sure if this is a bug or i am doing something wrong.<BR></BLOCKQUOTE><DIV><BR class="khtml-block-placeholder"></DIV>This was fixed in CVS a couple of days ago.<BR><BLOCKQUOTE type="cite"> <BR> By the way, As I have read from levitt's protocols, ENCAD is used with ATOM based nb interactions, and they use their own cutoff scheme, very similar to B.BrooKs's Force shifted spherical cutoff. Is it posible to use that protocols? How can be selected in a mdp file? I have not found info regarding that.<BR> </BLOCKQUOTE></DIV><DIV><BR class="khtml-block-placeholder"></DIV>Actually, the original Encad setup is even more complicated, since it uses a group-based 1,4 interaction scaling.<DIV><BR class="khtml-block-placeholder"></DIV><DIV>Michael (Levitt, encad author) and I have worked together to parameterize and check things, and we're both perfectly happy with the charge group setup currently used in the Gromacs Encad version.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Although the Encad program by default uses shifted interactions with a cutoff at 6A and rlist to 8A, the encad *force field* was not explicitly parameterized for that. We're currently testing how it performs with PME, but you can use "encadshift" for both coulombtype and vdwtype with the cutoff/rlist above if you want.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Cheers,</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Erik </DIV><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; "><DIV>-----------------------------------------------------------</DIV><DIV>Erik Lindahl <<A href="mailto:lindahl@sbc.su.se">lindahl@sbc.su.se</A>></DIV><DIV>Assistant Professor, Stockholm Bioinformatics Center</DIV><DIV>Stockholm University, SE 106 91 Stockholm</DIV><DIV>Phone: +46 8 5537 8564 Fax: +46 8 5537 8214</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><BR class="Apple-interchange-newline"></SPAN> </DIV><BR></DIV></DIV></BODY></HTML>