This is exactly what I've obtained http://imageshack.us/photo/my-images/27/89293914.png/
the same effect was also in case of intact tieleman's lipid bilayers ( the water layers were broader than lipid after resizing with genbox) James 2012/10/2, Justin Lemkul <jalem...@vt.edu>: > > > On 10/2/12 3:49 PM, James Starlight wrote: >> 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). >> > > Posting a link to an actual image would be really useful here. I'm not sure > I > understand your metaphor exactly. > > If you're looking to add lipids and water around an existing system, the > z-dimension of the solute and solvent boxes have to be the same. So if you > have > a system that you have extended in z to accommodate a protein or whatever > else, > you need to manipulate a DPPC-only system in the same way - extend its > z-dimension to be the same as the "solute," maintaining the relative > position of > the membrane within the new "solvent" box, and then add water in the > "solvent" > configuration to fill that box. Then proceed as I've suggested before. It > > should be obvious from all of this that it is vastly easier to plan a box of > > sufficient size before starting ;) > > -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