hello everyone i used editconf editconf -f protein.gro -o protein_newbox.gro -box (membrane box vectors) -center *x y z*
but in z axis i have been increased box size 10.0000 (previously it is 6.23910 6.17970 6.91950 http://s48.photobucket.com/user/mittukhattri/media/ri_zpsbb51fbd7.png.html?filters[user]=140927090&filters[recent]=1&sort=1&o=0 this is the em.gro first minimization image mixing of lipid and protein molecule kindly help On Fri, Jul 25, 2014 at 7:17 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/24/14, 11:57 AM, RINU KHATTRI wrote: > >> hello everyone >> thank you justin >> i did the same >> till minimization without the ligand it is in the lipid and center but i >> edit the box size arbitrary i used x and y axis as present in popc but in >> z >> axis used 10.00000 so there is overlapping of protein and lipid i think >> this can create problem >> > > I don't understand if there is a question or problem here. If something > is wrong, provide the exact command(s) used and provide images of the > undesirable output. Without that information, there's nothing that I or > anyone else can do to help you. > > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.