Justin Previously I've expanded initial system on Z-dim before the protein was inserted to increase both water layers.
After current processing with Genbox there is no problems in Z actually- it look likes sandwich with two broader bread layers and narrower cutlet :) So the lipid layer in x and y is thinker than water ( so the lipid number stay the same after resizing). James 2012/10/2, Justin Lemkul <jalem...@vt.edu>: > > > On 10/2/12 2:56 PM, James Starlight wrote: >> Justin, >> >> I've done exactly like you provide me ( changing only x and y ) >> >> but in that case the protein and the old lipids were slightly shifted >> to one side of the new system. Is there any way to center the old >> system in respect to the new solvent ? >> > > Define a new box and center with editconf -c -box. > >> Also I've noticed that when I increase size of my system in x and y >> dimensions both of the water layers were increased greatly than lipid >> layer ( it's look like sandwich with two big bread pieces and smaller >> cutlet between them :) ) >> > > This suggests that something is wrong with the z-dimension. I only say that > > because you had a 10-nm z-length in your previous post with the Tieleman > DPPC > bilayer, which is far larger than the coordinate file normally has. genbox > > works by tiling the solvent coordinates through the empty space in the > solute > configuration. If you're expanding in 3 dimensions, you can expect weird > things > to happen with membrane systems. > > -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 > > ======================================== > -- > 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