Thanks Andreas. Is there any difference force-wise between this and our little workaround?
Alex On Mon, May 3, 2010 at 2:17 PM, Kukol, Andreas <a.ku...@herts.ac.uk> wrote: > Hi, > > The POPC_53a6 topology works only with Gromacs versions lower than 4. > Please find attached the topology compatible with Gromacs4. > > I shall update files on the Gromacs website. Sorry for causing confusion. > > Best wishes > Andreas > > ________________________________________ > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On > Behalf Of Alex Smolyanitsky [asmol...@asu.edu] > Sent: 03 May 2010 18:22 > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] POPC 53a6 topology (dihedral multiplicity) > > Yup, those are indeed constants associated with phi2 (Fig. 1(B)), thanks. > > 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. > On Mon, May 3, 2010 at 10:57 AM, XAvier Periole <x.peri...@rug.nl<mailto: > x.peri...@rug.nl>> wrote: > > HAve look at the paper describing the topology ... > > > On May 3, 2010, at 6:52 PM, Alex Smolyanitsky wrote: > > Hello everyone, > > I am trying to include a POPC 53a6 topology from LipidsForGro96_53a6.zip ( > http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies) > for a simple lipid in water sim (gromacs version 4.0.5). > > I am using the lipid coordinates from the same archive and here's my > topology: > *** > #include "ffG53a6.itp" > #include "popc_53a6.itp" > #include "spc.itp" > > [ system ] > ;Name > test > > [ molecules ] > POPC 128 > SOL 3585 > *** > > 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. > The error has to do with two dihedral angles with zero multiplicity: > > ... > 22 23 24 25 1 90 -5.685 0 > ... > 24 25 26 27 1 90 -5.685 0 > ... > > So I looked at an ancient POPC topology for GROMOS87 and these dihedrals > have zero equilibrium angle and a multiplicity of 3: > > ... > 22 23 24 25 1 0.0 5.858 3 > ... > 24 25 26 27 1 0.0 5.858 3 > ... > > 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. > > Alex > -- > gmx-users mailing list gmx-users@gromacs.org<mailto: > gmx-users@gromacs.org> > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org<mailto: > gmx-users-requ...@gromacs.org>. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > gmx-users mailing list gmx-users@gromacs.org<mailto: > gmx-users@gromacs.org> > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org<mailto: > gmx-users-requ...@gromacs.org>. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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