Thank Justin ! I used the command "editconf -center" and i saw my membrane was in center of the box. I am stupid in that how putting the bilayer in a periodic image (instead between two periodic images as it was). Can you give me some instructions ? Many thanks !
On Fri, Apr 12, 2013 at 6:52 PM, Justin Lemkul <jalem...@vt.edu> wrote: > On Fri, Apr 12, 2013 at 7:48 AM, Kieu Thu Nguyen <kieuthu2...@gmail.com > >wrote: > > > Dear All, > > > > I made a POPC bilayer and carried out embedding a protein into this > > membrane. But the fatal error has appeared : > > Fatal error: > > Something is wrong with your membrane. Max and min z values are 12.342000 > > and 0.016000. Maybe your membrane is not centered in the box, but located > > at the box edge in the z-direction, so that one membrane is distributed > > over two periodic box images. Another possibility is that your water > layer > > is not thick enough. > > > > I think my bilayer stay at between two periodic images. What should i do > to > > put it in corrected position ? > > > > > It should be a very simple matter of visualization. Use editconf -center to > place the membrane wherever you want within the unit cell. You can remove > the uncertainty ("I think" is weak compared to "I know") by looking at the > box vectors and then numerically determining the center of the membrane > with g_traj. That should provide you with all the information you need to > determine what's going on. > > -Justin > > -- > > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) > 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 > -- 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