Thanks Justin I'll try to do that things.
Some addition questions 1) About nvt and apt equilibration As I understood ref_t of the system must be equal to temperature of the phase transition of the specific LIPID. But in the npt and nvt.mdp files there are severl enties for ref_t ( for some system groups in index.ndx ) For my system composed of protein dmpc and water : ref_t = 323 297 323 ; Does all this values in mdp file must be equal ( to the temperature of the lipid phase transition) ref_t = 297 297 297 or each value must correspond to the temperature of phase transition of the individual element ? ref_t = 323 297 323 ; Does thic correct for both NPT and NVT ensembles ? James 2011/11/11 Justin A. Lemkul <jalem...@vt.edu> > > > James Starlight wrote: > >> Justin, >> >> Could you tell me what difference in inflategro parameters ( cut-off for >> lipid removing and scaling factors) should I make for insertion protein in >> another bilayes in comparison tu tutorial ? >> >> > I've never made any changes; it's always worked just fine. > > > Now I'm working with DMPC. I've inserted symmetrical alpha helices >> protein in this bilayer but inflategro deleate 2 lipid from upper and just >> 1 from lower layer. It's strange because I suppose that equal bilayer >> molecules would be removed :o >> >> > The number of lipids that are removed will depend on the starting > configuration of the membrane and thus where lipids are relative to the > protein. Theoretically, a symmetrical protein should delete an equal number > of lipids from each leaflet, if the geometry of the top and bottom leaflets > is comparable. Either try placing the protein at a different location to > achieve equivalent removal or manually delete a lipid and be sure to > equilibrate adequately. > > > >> On Inflategro's sites I havenot found such specifity for above parameters >> for different bilayers :( >> > > The cutoffs specified are simple grid search parameters. They do not > necessarily need to be altered depending upon the lipid type. > > > -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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