<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="font-size: 10pt; font-family: verdana; "><div><font face="Verdana" size="2">I'm trying a coarse-grained simulation with three beads representing the backbone structure of each residue. However, it's difficult to get the LJ parameters for -NH- and -CO- . Could anyone possibly know some work on this?</font></div></div></span></blockquote>Well, there is no magic parameters for NH or CO for a Coarse-grain simulation!</div><div>These would be effective interaction and therefore depend entirely of the rest</div><div>of the interaction you are using!</div><div>You'll have to parameterize them to reproduce data that you think relevant.</div><div><br></div><div>It is a very vague answer, sorry, but your question suggests that you should</div><div>try some literature on the subject force field parameterization and coarse-graining.</div><div><br></div><div>hope this helps.</div><div>XAvier.</div><div><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="font-size: 10pt; font-family: verdana; "><div> </div><div><font face="Verdana" size="2">Thanks in advance.</font></div><div><font face="Verdana" size="2"></font> </div><div align="left"><font face="Verdana" color="#c0c0c0" size="2">Cristty</font></div>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><span class="Apple-converted-space"> </span>before posting!<br>Please don't post (un)subscribe requests to the list. Use the<span class="Apple-converted-space"> </span><br>www interface or send it to<span class="Apple-converted-space"> </span><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a></div></span></blockquote></div><br></body></html>