Mark, Firstly I've downloaded Berger's dppc.itp and dppc.gro ( I've already have had gromos lipid ff)
than I made pdb file for just 1 molecule of the dppc lipid consisted of 50 atoms and generate for that new molecule lipid_posres.itp via pdb2gmx than I've included lipid_posre.itp to the dppc.itp at the end of file where the reference for the posres_lipid was already existed as POSRES_LIPID. I've included in the minim.mdp define= - DPOSRES_LIPID than I've minimized my bilayer dppc.gro and checked by VMD if the bilayer was perturbed after simulation So althought posres were included in the minim.pdb the bilayer was perturbed ( tails of lipids were less ordered in comprison to the initial bilayer ) Why posres didnt work? 2011/11/2 Mark Abraham <mark.abra...@anu.edu.au> > > > On 02/11/11, *James Starlight *<jmsstarli...@gmail.com> wrote: > > 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 ? > > > We can't know, because we don't know what's in any files, nor why you > think the bilayer was perturbed. If you would like useful help, you need to > be exhaustive in your description of what you have done, what you have > observed and what you think about those. It is easier for people who might > volunteer free help to do something else with their time than to ask > follow-up questions when few details were given originally. > > Mark > > > > > 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> >> > > > > -- > 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/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 >
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