<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div>HAve look at the paper describing the topology ... <div><br></div><div><br><div><div>On May 3, 2010, at 6:52 PM, Alex Smolyanitsky wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hello everyone,</div> <div> </div> <div>I am trying to include a POPC 53a6 topology from LipidsForGro96_53a6.zip ( <a href="http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies" target="_blank"><font color="#2a5db0">http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies</font></a> ) for a simple lipid in water sim (gromacs version 4.0.5).</div> <div> </div> <div>I am using the lipid coordinates from the same archive and here's my topology:</div> <div>***</div> <div>#include "ffG53a6.itp"</div> <div>#include "popc_53a6.itp"</div> <div>#include "spc.itp"</div> <div> </div> <div>[ system ]</div> <div>;Name</div> <div>test</div> <div> </div> <div>[ molecules ]</div> <div>POPC 128</div> <div>SOL 3585</div> <div>***</div> <div> </div> <div>grompp throws a fatal error: " Value of 'multiplicity' in Proper Dih. is 0, which is smaller than the minimum of 1" without any prior warnings. </div> <div>The error has to do with two dihedral angles with zero multiplicity:</div> <div> </div> <div>...</div> <div>22 23 24 25 1 90 -5.685 0</div> <div>...</div> <div>24 25 26 27 1 90 -5.685 0</div> <div>...</div> <div> </div> <div>So I looked at an ancient POPC topology for GROMOS87 and these dihedrals have zero equilibrium angle and a multiplicity of 3:</div> <div> </div> <div> <div>...</div> <div>22 23 24 25 1 0.0 5.858 3</div> <div>...</div> <div>24 25 26 27 1 0.0 5.858 3</div> <div>...</div> <div> </div> <div>Did the author of the 53a6 topology want to simply remove these dihedrals by setting a multiplicity of zero? Or, should these two be set according to the older topology? I know similar questions have been asked here in the past, but I really want to make sure my topology is sane. Thanks a lot.</div> <div> </div> <div>Alex</div></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 http://www.gromacs.org/search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/mailing_lists/users.php</blockquote></div><br></div></body></html>