Hi Jonas, Do you mean atomistic or coarse grained? Of course you should mean coarse grained as it's out of the question to reach equilibration for a significant amount of lipids with such complexity, which will take several microseconds. I have a tool for building membranes, which could be of value. You can contact me off list if you want.
Cheers, Tsjerk On Fri, Nov 2, 2012 at 4:21 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/2/12 11:15 AM, jonas87 wrote: > >> Dear all, >> >> I wish to run a simulation of a membrane consisting of about 10 different >> lipids. >> Through the automated topology builder ( example >> <http://compbio.biosci.uq.edu.**au/atb/download.py?molid=1556<http://compbio.biosci.uq.edu.au/atb/download.py?molid=1556>> >> ) I can obtain >> of each lipid a structure file in pdb format (it has one single molecule) >> and an .itp topology file. >> I want to make a random mix of these lipids with water and let it >> equilibrate over 300 us or so to let it assemble into a bilayer. >> My question is, how can I combine all these structures and topologies into >> one system that has X molecules of lipid A, Y molecules of lipid B, etc. I >> think genbox might have the answer for combining the sructures, but how? >> > > Building lipid membranes is complicated. In theory, you could position > individual molecules in specific orientations within a given box with > editconf to form patches that can then be translated and rotated in any way > you desire, or replicated with genconf -nbox. I have only ever done this > for a single-component lipid membranes. > > The topology is actually easier. After #including the parent force field, > you simply #include each lipid topology individually. The [molecules] > section then must reflect the contents of the coordinate file with respect > to the number of molecules and the order they appear. > > > Also, if someone could point me towards a tutorial were they let a >> membrane >> form from a random distribution of a lipid with water that would be >> useful. >> The only GROMACS membrane tutorials that I can find always start with >> pre-equilibrated membranes of 128 DOPC molecules. >> >> > To my knowledge, there is no such tutorial (if it's not on the Tutorials > page or found via Google, it doesn't exist). You can randomly insert > molecules into a box with genbox -ci -nmol and then fill with solvent later. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > 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> > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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
