Justin,
lastly, is there any other ways to obtain bilayers of desired dimensions started from just one lipid oriented in desired way for instance? James 2012/10/3, Justin Lemkul <jalem...@vt.edu>: > > > On 10/3/12 12:38 PM, James Starlight wrote: >> Justin, >> >> thanks for advises. >> >> Finally how I could effectively reduce size of my system (in x and y ) >> to the defined pbc box size ( see picture to the previous comment) ? >> >> I've noticed that increasing of x and y to the 12 nm I obtain ideal >> shape of the bilayer without miss-matches of the left and right sizes. >> But when I try to decrease dimensions of that system from 12 to 8 nm >> >> genbox -cs xz.gro -box 8.04542 8.04542 10.19156 >> >> I've obtained the system with the broadered water layers again ( as in >> the picture which I've shown). >> > > My advice is still the same - you need box vectors that are compatible with > both > a sensible water layer and membrane leaflets. > > -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