I have used editconf -f protein.gro -c -bt cubic -d 1.5 -o confout.gro to set the box.
Then genbox -cp confout.gro -cs dppc128.gro -o protein_in_membrane.gro got hanged Am I missing something here??? On Tue, Jun 10, 2014 at 2:51 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/9/14, 9:08 AM, Venkat Reddy wrote: > >> Dear Justin, >> I have tried the command >> genbox -cp protein.gro -cs membrane.gro -o protein_in_membrane.gro >> but it got hanged. Is there something wrong with the command? >> >> > I wouldn't expect a hang as long as the box is set to appropriate > dimensions. The new box for the protein shouldn't be substantially larger > than the membrane itself. > > > -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. > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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.