Hi, Thanks for the question, and particularly the detail. It seems that you are trying use a [dihedraltypes] section in my_molecule.itp, which is generally a bad idea, because all such directives must appear before the first [molecule] directive, which defeats the point of molecule.itp files being somewhat movable. Because of that intention for molecule.itp files, there'd be no reason to have separate [dihedraltypes] sections that should be logically treated together, so the code assumes such sections are separable, and so you get unintended behaviour (perhaps particularly with wildcard atom types, and/or type 9 dihedrals) unless you change ffbonded.itp like you have now done.
Recommended procedures are * to copy the charmm36.ff directory into your working directory and modify ffbonded.itp to work like you want it to, or * to give explicit parameters in the [dihedrals] section of your molecule.itp (*not* [dihedraltypes]), so that the parameter lookup from [dihedraltypes] is not invoked at all. Note that the behaviour for multiple matching [dihedrals] is to add the functions; the behaviour for multiple matching [dihedraltypes] is to override earlier functions (except for type 9). Mark On Thu, Jan 9, 2014 at 2:30 PM, hubert santuz <hubert.san...@gmail.com>wrote: > Dear Gromacs Users, > > I'm trying to set up a molecule into the charmm36 force field for lipids. > I correctly obtained a good itp file from a charmm file. > In this itp file, a wildcard dihedraltype (from the ffbonded.itp) is > overrided by an explicit dihedraltype : > > In ffbonded.itp : > X CTL1 CTL2 X 9 0.00 0.8368 3 > In my itp file: > CRL1 CTL1 CTL2 CTL2 9 180.00 0.50961 3 > CRL1 CTL1 CTL2 CTL2 9 180.00 0.91002 2 > CRL1 CTL1 CTL2 CTL2 9 180.00 1.00332 1 > > In my topol.top: > #include "charmm36.ff/forcefield.itp" > #include "my_molecule.itp" > > > Unfortunately, this override is not taking in account by gromacs. > When I dump the tpr, I do not see this 3 types in the "functype" lines. > However, when I add this override into the ffbonded.itp file before the > wildcard dihedraltype like this : > > In ffbonded.itp: > CRL1 CTL1 CTL2 CTL2 9 180.00 0.50961 3 > CRL1 CTL1 CTL2 CTL2 9 180.00 0.91002 2 > CRL1 CTL1 CTL2 CTL2 9 180.00 1.00332 1 > X CTL1 CTL2 X 9 0.00 0.8368 3 > > In this case, I can see clearly the 3 dihedraltypes in my tpr. > > More interestingly, when I try to override an explicit dihedral type from > ffbonded.itp (like CEL1 CTL2 CEL1 HEL1) into my itp file, I get a warning > from grompp and I see the override in the tpr file. > It seems that wildcard dihedral types cannot be override (at least with > the function 9, I didn't test with other forcefields). > > For the moment, the only solution that I have found is either to : > - add the override in the ffbonded.itp which is not a good idea. > - or add 2 new atoms with new names but with the same parameters than > (CTL1 and CTL2) in my itp file and change the dihedraltype according to > these two new atoms. > > Without this override, I'm not able to reproduce the correct dihedral > energy from a SPE calculation between gromacs and namd... (but with the > override, I am!) > > Have people already experienced this case ? > Also, I can provide test files (itp, top, pdb) with only 4 atoms and this > dihedral. > > Thanks for the help! > Best regards, > > Hubert > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.