[gmx-users] Remove all but N closest water molecules from protein

[João Henriques]

Thanks for the clarification.

João

On Thu, Jun 8, 2017 at 11:58 AM, Mark Abraham <mark.j.abraham at 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.henriques at 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.abraham at 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.henriques at 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 tool that does all of this in one step but I may be outdated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" <borreguero at 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
> > > > --
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