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

[Jose Borreguero]

Hi Mark,

The following lines select solvent molecules within some cutoff distance of
the protein:

close_solvent_atoms = group "SOL" and within 0.5 of group "Protein";
close_solvent_molecules = same resindex as close_solvent_atoms;
"strippedSystem" group "Protein" or close_solvent_molecules;

It's not exactly what I wanted, butI can select N closest water molecules
by tuning the cutoff distance.

.Jose

On Thu, Jun 8, 2017 at 4:34 AM, Mark Abraham 
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 tool that does all of this in one step but I may be outdated regarding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"  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!
> >
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> >
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> send
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Re: [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 
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 
> > 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" 
> > 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!
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Re: [gmx-users] Remove all but N closest water molecules from protein

[Mark Abraham]

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 
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 
> 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" 
> 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.
> > --
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> >
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Re: [gmx-users] Remove all but N closest water molecules from protein

[João Henriques]

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 
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"  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!
> >
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> > send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Remove all but N closest water molecules from protein

[Mark Abraham]

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 
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"  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.
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>
> * Please search the archive at
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> posting!
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Re: [gmx-users] Remove all but N closest water molecules from protein

[João Henriques]

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

[Jose Borreguero]

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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