Hi again, Thank you very much for your reply Mark. Now, I have a dihedral with the following form: 22 23 24 25 1 0.0 7.47 1 22 23 24 25 1 0.0 3.9 2 22 23 24 25 1 180.0 1.1 3 22 23 24 25 1 0.0 -2.8425 0
Of course the "problematic" multiplicity of 0 just subtracts 5.685 from the energy. Would it then be OK to simply delete this line? I suppose it would be OK as it just adds a constant to the energy but I'm not 100% certain if it would give any problems with the calculation of forces. Sarah Sarah Witzke wrote: > Dear gromacs users, > > I'm doing simulations of small molecules in lipid bilayers. Doing the > simulations with a DMPC bilayer works fine for all 4.x versions of gromacs. > But when I try to do an energy minimization of a POPC bilayer, grompp gives > the following error: > > /people/disk2/sarah/gromacs-4.0.3/bin/grompp -f em.mdp -c system.gro -p > popcpalc32.top -o test.tpr > > Ignoring obsolete mdp entry 'cpp' > checking input for internal consistency... > processing topology... > Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/ffgmxnb.itp > Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/ffgmxbon.itp > Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/ff_dum.itp > Generated 1502 of the 2346 non-bonded parameter combinations > Generating 1-4 interactions: fudge = 1 > Generated 1068 of the 2346 1-4 parameter combinations > Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/flexspc.itp > Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/spc.itp > Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/ions.itp > Excluding 3 bonded neighbours molecule type 'PALC' > turning all bonds into constraints... > Excluding 3 bonded neighbours molecule type 'POPC' > turning all bonds into constraints... > Excluding 2 bonded neighbours molecule type 'SOL' > turning all bonds into constraints... > processing coordinates... > double-checking input for internal consistency... > renumbering atomtypes... > converting bonded parameters... > > ------------------------------------------------------- > Program grompp, VERSION 4.0.3 > Source code file: convparm.c, line: 68 > > Fatal error: > Value of 'multiplicity' in Proper Dih. is 0, which is smaller than the > minimum of 1 > ------------------------------------------------------- > > When looking through the lipid .itp file (popc.itp) I do see dihedrals with > multiplicity of 0 (which is not the case in dmpc.itp) - I haven't made it > myself but it has been used many times before. > > When running grompp in version 3.3.3 I get no error message: Yup - there was no test for validity of the input. Since a proper dihedral with multiplicity of zero is just a constant (see manual eq 4.61), it does nothing at all to the forces, nothing meaningful to energies and nothing to energy differences. Other than a convenient way to "comment out" dihedrals (which would be better done with a real comment!) I can't see the purpose of such dihedrals of multiplicity zero. Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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