Justin, Mark, Ok not I've included posre only to the lipid.itp wich consist of parameters for just 1 lipid
#ifdef POSRES_LIPID #include "posre_lipid.itp" #endif to the minim.mdp I've included define = -DPOSRES_LIPID ; position restrain the lipids As the result I have not obtained any error in grompp but after minimization my lipid bilayer was perturbed. I've used very strong posres. Why it have not worked ? 2011/10/31 Justin A. Lemkul <jalem...@vt.edu> > > > James Starlight wrote: > >> I've done all of that >> i have "posre_lipid.itp" - for 1 lipid ( posres for each of 50 atoms ) >> >> >> I've included this in the topology of the bilayer >> >> ; Include chain topologies >> #include "gromos53a6_lipid.ff/**forcefield.itp" >> #include "dppc.itp" >> >> ; Include water topology >> #include "gromos53a6_lipid.ff/spc.itp" >> >> ; Include ion topologies >> #include "gromos53a6_lipid.ff/ions.itp" >> >> #ifdef POSRES_LIPID >> #include "posre_lipid.itp" >> #endif >> >> ; System specifications >> [ system ] >> 128-Lipid DMPC Bilayer in water >> >> [ molecules ] >> ; molecule name nr. >> DPPC 64 >> SOL 1193 >> SOL 690 >> >> >> Also I've tried to make posre for whole system ( large posres ) but it >> also was finished with same error >> >> Fatal error: >> [ file posre_lipid.itp, line 6 ]: >> Atom index (2) in position_restraints out of bounds (1-1). >> This probably means that you have inserted topology section >> "position_restraints" >> in a part belonging to a different molecule than you intended to. >> In that case move the "position_restraints" section to the right molecule. >> For more information and tips for troubleshooting, please check the >> GROMACS >> website at >> http://www.gromacs.org/**Documentation/Errors<http://www.gromacs.org/Documentation/Errors> >> >> What's most true for such multy system. Generate posre only for 1 part or >> for whole system? >> >> > Position restraints can only be applied on a [moleculetype] basis. Thus, > order matters a lot, and the whole system cannot be restrained in one file. > See the example here: > > http://www.gromacs.org/**Documentation/Errors#Atom_**index_n_in_position_* > *restraints_out_of_bounds<http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds> > > As it stands now, the topology you've shown tries to apply lipid position > restraints after the ions have been #included, which makes no sense at all. > > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/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/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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