Justin,
Indeed GenBox added insufficien of the SOL to my system due to the ussage of increased vdvdat ( I've used 0.350 value for the c atoms only but the were alot of void beetwen water and bilayer ) lipid_posres in Z directions have prevented the displacement of the bilayer but the water were distruibuted irregular on the bilayer surface at the end of NVT phase By the way in Gmembed system I have no such problems because the were no need to use genbox but during processing of the system I've obtain warning WARNING 1 [file membed.mdp]: Can not exclude the lattice Coulomb energy between energy groups What does it mean? By the way could I indicate Area per lipid during processing of my system with the G_membed? James 2011/11/11 Justin A. Lemkul <jalem...@vt.edu> > > > James Starlight wrote: > >> Justin, >> >> The system was compact after inserting protein into bilayer (I've obtain >> Area per lipid in accordanc with experimental reference) and futher >> minimization (only some llipid tails on the border of the system were >> distorded alittle) >> But after nvt simulation this discrepancy occured :) >> >> I've used pbc size like in the KALP simulation because I have bilayer ( >> 128 lipids) and the protein (38 a.a) of the same size. >> > > KALP-15 has only 15 residues; your peptide is significantly longer. > > > My box vectors were 6.500 6.500 6.500 >> >> Do you think that I should use smaller pbc? How I could define pbc on the >> right size for my purely bilayer system? >> >> > You shouldn't use the box vectors I did in the tutorial - use the > dimensions present in the actual membrane you're using. I still see no > conceivable way that the bilayer separated that much during NVT without > significant empty space in the unit cell to start. In NVT, the volume is > constant, so if there are voids, the lipids will fill to expand them. I've > seen it countless times, so please be sure you're actually providing > sufficient solvent and an appropriate location for all your components > within the unit cell. > > -Justin > > I've used >> >> trjconv -s em.tpr -f dmpc128.gro -o dmpc128_whole.gro -pbc mol -ur compact >> >> at the preequilibrated bilayer and than done anything in accordance to >> the KALP tutorial >> >> >> James >> >> >> 2011/11/11 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>> >> >> >> How large of a void exists between your lipids and water prior to >> starting the simulation? I'm almost certain that you built the unit >> cell incorrectly - there should never be that much free space. >> >> >> >> By the way I'ts intresting that Gmembed has removed 6 lipids in >> comparison to the inflateglo ( althought I've done all things in >> accordance to the KALP tutorial because my protein is the same). >> >> >> Different algorithms, different results. Nothing odd about that to me. >> >> -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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