Justin, What temperature for NVT phase should be in
gen_temp = 323 Does this parameere must be equal to the ref_t ? I've obtain strange results after NVT with ref_t = 297 297 297 for protein in DMPC bilayer. The bilayer with water parts diffused in up and down direction of the box relative protein Why this should occur ? Might I alpy posres for lipid in NVT phase ? 2011/11/11 Justin A. Lemkul <jalem...@vt.edu> > > > James Starlight wrote: > >> 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 ? >> >> > It is incorrect to set different groups at different temperatures. > Whatever result you obtain would be completely unrealistic. > > -Justin > > >> James >> >> 2011/11/11 Justin A. Lemkul <jalem...@vt.edu <mailto: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 <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >> >> <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 >> <mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> >> <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> >> >> >> <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 >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >> >> >> > -- > ==============================**========== > > 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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