Hi, Or gmx select to make an index group for the nearest waters, and gmx trjconv to make the subset with the index group.
Mark On Thu, Jun 8, 2017 at 9:05 AM João Henriques <[email protected]> wrote: > Hi, > > trjorder can reorder the water molecules in each frame according to their > distance to the protein. Then you either manually prune the gro file(s) or > use an index file to get rid of the extra stuff. I don't know of any native > tool that does all of this in one step but I may be outdated regarding new > stuff on gmx 2016. > > Cheers, > João > > On Jun 8, 2017 2:49 AM, "Jose Borreguero" <[email protected]> wrote: > > Dear Gromacs users, > > I'm a newbie with Gromacs. Is there a Gromacs native tool that will allow > me to create a new *.gro file containing the protein and the N closest > water molecules to the protein > , starting from a system of a solvated protein > ? > > Best, > Jose Borreguero > -- > 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 [email protected]. > -- > 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 [email protected]. -- 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 [email protected].
