I guess I need to write [ exclusions ] as TUB is composed of other energygrps. I have 2516 atoms, that would be difficult to write [ exclusions ] manually, would you recommend any script? I am not programming :(
Steven On Thu, Dec 5, 2013 at 3:01 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 12/5/13 9:48 AM, Steven Neumann wrote: > >> Dear Gmx Users, >> >> How can I apply exclusions of non-bonded parameters within my >> [moleculetype] - I the positions of this molecule is restrained so all >> non-bonded should be excluded. Would that need [ exclusions ] or >> energy-monitor group can be applied? >> > > Either set nrexcl to a sufficiently large number that encompasses the > longest possible bonded geometry or write an [exclusions] directive > yourself. > > > what shall i specify >> energy-monitor group = TUB TUB >> >> > Assuming you mean energygrp-excl = TUB TUB, that would also work. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > 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 > > ================================================== > -- > 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.