Use "gmx editconf" first to create the box then "gmx solvate" to fill it with water (omitting -box directive this time).
-- James "Wes" Barnett Ph.D. Candidate Chemical and Biomolecular Engineering Tulane University Boggs Center for Energy and Biotechnology, Room 341-B New Orleans, Louisiana 70118 jbarn...@tulane.edu LinkedIn ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Vy Phan <phanvy120...@gmail.com> Sent: Thursday, May 21, 2015 8:36 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Generate the water box Dear all, I can generate the cubic box or the rectangular box with gmx solvate -cs water.gro -box but I would like to have the octahedron box.I try many way but I can not. How I can do it? Thank a lot Tuong Vy 2015-05-21 1:49 GMT+09:00 Justin Lemkul <jalem...@vt.edu>: > > > On 5/20/15 11:55 AM, 姚懿 wrote: > >> genbox without adding a protein. >> >> > More specifically (and for 5.0): > > gmx solvate -cs water.gro -box (whatever size is needed) > > -Justin > > On Wed, May 20, 2015 at 9:56 AM, Vy Phan <phanvy120...@gmail.com> wrote: >> >> Dear Gromacs Users, >>> >>> Can I generate only water on the Gromacs? I need water box only. >>> >>> Thank you >>> Tuong Vy >>> -- >>> 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. >>> >>> >> >> >> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > 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. -- 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.