[gmx-users] Regarding getting the coordinates within certain region of amino-acid

[Dilip.H.N]

I tried the following two ways ie., with gmx select and with gmx trjorder

1) when i give the command :-
gmx trjorder -f nptmd.xtc -s nptmd.tpr -n ndx_all.ndx -o order.gro -nshell
-r 0.35

i got an output file, it has all the water molecules (i have 511 water
molecules in my system) for each time frame but it has arranged according
to the smallest distance to atoms in the reference group. (but i want only
those water molecules within 0.35nm of nitrogen of glycine molecule.)

2) in this command:-
gmx select -f nptmd.xtc -s nptmd.tpr -n ndx_all.ndx -oi -select '"close to
name N" resname SOL and within 0.35 of group protein'

i am getting an .dat file which has only the coordinates and the format on
as in index file format.

Actually, i wanted the format in which the gmx trjorder output gives (as in
my case, order.gro), but i want only those water molecules which are within
3.5 nm of the nitrogen atom of glycine molecule for each time frame.

Any suggestions are appreciated.

Thank you.

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---
With Best Regards,

Dilip.H.N
PhD Student.

On Wed, Apr 11, 2018 at 6:23 PM, Marc Hoemberger <hoemberg at brandeis.edu>
wrote:

> You can use either gmx trjorder with the nshell parameter (if it is as
> simple as within Xnm of Y, use nshell parameter, see manual) or gmx select
> (if you need some more complex selection).
>
> On Wed, Apr 11, 2018 at 3:54 AM, Dilip.H.N <cy16f01.dilip at nitk.edu.in>
> wrote:
>
> > Hello all,
> >
> > I want to get the water molecules which are at a certain distance (say
> all
> > the water molecules which are within 0.35nm of the Nitrogen atom of
> glycine
> > molecule). How can i get this all the coordinates.?
> >
> > Any specific commands..??
> >
> >
> > Thank you.
> >
> > ---
> > With Best Regards,
> >
> > Dilip.H.N
> > PhD Student.
> > <https://mailtrack.io/> Sent with Mailtrack
> > <https://mailtrack.io?utm_source=gmail&utm_medium=
> signature&utm_campaign=
> > signaturevirality&>
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> --
> Marc Hoemberger
> Ph.D. Candidate, Biochemistry and Biophysics,
> Laboratory of Dorothee Kern
> MS-009, 415 South St.
> Brandeis University
> Waltham, MA, 02453
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