But mdrun doesnt update these information/new numbering in the topology file. I mean the topology fie would be saying that there is a bond between 101 and 105 and if I removed those atoms, the mdrun would have assignmed 101 and 105 to some other atom and hence it can create problems.
Is this possible? On Wed, Jul 16, 2014 at 9:35 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/15/14, 2:19 PM, vivek sinha wrote: > >> Hey Justin, >> I think I understood the problem. When I removed the solvent from inside >> CNT, I kept the numbering of atoms just like before without actually >> making >> a new strictly increasing order numbering. But now when I see that after >> the energy minimization the new pdb file got arranged strictly by >> increasing order. >> >> As an example. After deleting atoms inside the CNT, my .gro file did not >> had the atom no 6292, but after energy minimisation the em.gro file >> contains the atom no 6292. This must have created a renumbering of the >> atoms. Not good I suppose. >> Please suggest what to do? >> >> The concern is that whether to renumber the molecules after removing the >> water from inside the CNT or not? >> >> > The numbering in the input coordinate file is irrelevant. The output of > mdrun is always numbered consecutively from 1. > > > -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.