Hi Mark, Does your solution output variable numbers of water molecules per frame? That is exactly what I've been wanting to do for a while, but with my solution it becomes very difficult to do so and I usually end up using a fixed number of closest waters for all frames.
João On Thu, Jun 8, 2017 at 10:34 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > 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 < > joao.m.a.henriq...@gmail.com> > 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 tool that does all of this in one step but I may be outdated regarding 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" <borregu...@gmail.com> 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 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.