<div>Yup, those are indeed constants associated with phi2 (Fig. 1(B)), thanks.</div>
<div> </div>
<div>Just in case anyone else is faced with the same issue, as far as forces are concerned, these dihedrals can be commented out. When considering the energy associated with dihedrals, just shift it appropriately.<br></div>
<div class="gmail_quote">On Mon, May 3, 2010 at 10:57 AM, XAvier Periole <span dir="ltr"><<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div style="WORD-WRAP: break-word">
<div><br></div>HAve look at the paper describing the topology ...
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<div><br>
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<div></div>
<div class="h5">
<div>On May 3, 2010, at 6:52 PM, Alex Smolyanitsky wrote:</div><br></div></div>
<blockquote type="cite">
<div>
<div></div>
<div class="h5">
<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></div></div>-- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a></blockquote></div><br></div></div><br>--<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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</blockquote></div><br>