Justin, I've found the same task of MSU's students :) They simulate membrane formation without NPT stage ( after NVT they run production MD). From they reports I've found that simplest membrane system could be formed within 10-30 Ns. But what about try to make such simulation in vacuum at first without any water ? Might the bilayer been formed in such conditions?
Finally I have small question about pereodic boundaries of such bilayer system. E.g I've done simplest system with water consisted of 8 lipid molecules + some water. This is the representation of the system http://i1209.photobucket.com/albums/cc394/own11/lipids8.png I want to simulate bilayer formation as well as concomitant hydrophobic effect ( removing all water from formed bilayer) Does the PBC presented in that example ( 2.64196 2.64196 6.85002 for 8 lipids) are enought for such lipid movement? It seems that more free space aree needed for overal turn of lipid molecules. How I can calculate exactly PBC value required for my system ? James 2011/10/25 Justin A. Lemkul <jalem...@vt.edu> > > > James Starlight wrote: > >> Justin, >> >> Could you tell me if I want to simulate self-organization of the pure >> lipid bilayer starting from the initial random placed molecules in water. >> Does this simulation need in pre-md NVT and NPT equilibration? >> > > Some form of equilibration is always required. > > > What the average time for NPT? I think that If this stage should occur it >> must be consist of long ( tens of NS ) preequilibration. >> >> >> > Temperature and pressure will likely converge within a few ns, but the > simulation is not equilibrated until the membrane has formed, I would say. > This is a process that can take hundreds of ns, or even us. Check the > literature for established protocols; there are reports of bilayer > self-assembly already published. > > -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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