Thanks for the clarification. João
On Thu, Jun 8, 2017 at 11:58 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > No. gmx select will write index groups that could implement a dynamic > selection, but trjconv can't do anything sensible with it. You'd have to > split the trajectory into a file per frame and match the index group to the > file to get the selection into a new file. Even if trjconv was smart > enough, you'd also need to use a trajectory format and downstream tools > that were about to be flexible about the number of atoms (which is > typically not the case)... In principle, our TNG format is able to be > flexible, but there's a lot of infrastructure work if people would actually > write such files and expect to read them and have everything work well. > Better to work on tools that can use the dynamic selection without needing > to serialize and de-serialize files (and the new GROMACS analysis framework > has such support, but we don't have much funding for implementing / porting > tools to it). > > Mark > > On Thu, Jun 8, 2017 at 10:48 AM João Henriques < > joao.m.a.henriq...@gmail.com> > wrote: > > > 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 tool that does all of this in one step but I may be outdated 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? 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