Thanks Mark, but I hardly believe that helps. What you suggest can work for only one frame. But I need a selection which works at the same time for all frames (in my loop over trajectory), where there are no molecules at some frames or two or more at others (in z >= 10 and z <= 10.1).
Best regards On Fri, Jul 15, 2016 at 6:48 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > If your criterion could satisfy more than one molecule but you for example > only want the first one, then you can likely create a second selection > where you filter out from the first selection the molecule or atom indices > that suit you. I assume that can be done in one call to gmx select, but the > details are an exercise for the reader :-P > > Mark > > On Fri, 15 Jul 2016 15:52 Faezeh Pousaneh <fpoosa...@gmail.com> wrote: > > > I undrestand my command is not correct for having one water. So it is my > > question how to change the command to have a single molecule? > > > > > > > > Best regards > > > > > > On Fri, Jul 15, 2016 at 3:35 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > > > > > On 7/15/16 9:28 AM, Faezeh Pousaneh wrote: > > > > > >> Hi, > > >> > > >> I want to select only a 'single' water molecule at specific part of my > > >> simulation box. > > >> So I try: > > >> > > >> g_select -selrpos whole_mol_com > > >> > > >> and select > > >> > > >> resname SOL and z >= 10 and z <= 10.1 > > >> > > >> But depending on time frame I get more than one molecules or sometimes > > no > > >> molecules. How can I fix it? > > >> > > >> > > > Why do you think that the selection criteria should always return > exactly > > > one water? I see no reason to think that based on what your syntax > > > specifies. > > > > > > -Justin > > > > > > -- > > > ================================================== > > > > > > 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. > -- 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.