The -on option too gives the output as in index format, which i don't want.
I want it in a .gro file and not as in an index file format.In gmx select
options the output files are written in .xvg/.ndx.dat format only...
i want the output to be written like the following:-

frame t= 0.000
 1543
    1GLY      N    1   1.206   1.052   1.131
    1GLY     H1    2   1.266   1.070   1.215
    1GLY     H2    3   1.270   1.019   1.056
    1GLY     H3    4   1.134   0.981   1.155
    1GLY     CA    5   1.158   1.191   1.103
    1GLY    HA1    6   1.086   1.211   1.181
    1GLY    HA2    7   1.127   1.205   1.001
    1GLY      C    8   1.276   1.289   1.123
    1GLY    OT1    9   1.252   1.408   1.108
    1GLY    OT2   10   1.392   1.257   1.149
  253SOL     OW  764   1.085   0.998   0.837
  253SOL    HW1  765   0.998   0.982   0.883
  253SOL    HW2  766   1.109   0.919   0.781
  252SOL     OW  761   0.848   1.089   0.990
  252SOL    HW1  762   0.767   1.098   1.049
  252SOL    HW2  763   0.881   1.180   0.965
.
.
frame t= 1.000
 1543
    1GLY      N    1   1.229   1.032   1.106
    1GLY     H1    2   1.277   1.040   1.198
    1GLY     H2    3   1.290   0.979   1.041
    1GLY     H3    4   1.145   0.976   1.127
    1GLY     CA    5   1.198   1.175   1.059
    1GLY    HA1    6   1.128   1.213   1.132
    1GLY    HA2    7   1.175   1.175   0.953
    1GLY      C    8   1.309   1.273   1.082
    1GLY    OT1    9   1.282   1.393   1.056
    1GLY    OT2   10   1.417   1.237   1.137
  155SOL     OW  470   1.005   1.448   1.113
  155SOL    HW1  471   1.103   1.445   1.095
  155SOL    HW2  472   0.957   1.477   1.030
  388SOL     OW 1169   1.307   1.001   1.370
  388SOL    HW1 1170   1.329   1.053   1.452 etc...

Any suggestions are appreciated.

Thank you.
‌
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---
With Best Regards,

Dilip.H.N
PhD Student.

On Thu, Apr 12, 2018 at 1:12 PM, Joe Jordan <e.jjorda...@gmail.com> wrote:

> You need -on for gmx select to write out the index file.
>
> On Thu, Apr 12, 2018 at 8:48 AM, Dilip.H.N <cy16f01.di...@nitk.edu.in>
> wrote:
>
> > 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.
> >
> > ‌
> > <https://mailtrack.io/> Sent with Mailtrack
> > <https://mailtrack.io?utm_source=gmail&utm_medium=
> signature&utm_campaign=
> > signaturevirality&>
> >
> > ---
> > With Best Regards,
> >
> > Dilip.H.N
> > PhD Student.
> >
> > On Wed, Apr 11, 2018 at 6:23 PM, Marc Hoemberger <hoemb...@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.di...@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&>
> > > > --
> > > > Gromacs Users mailing list
> > > >
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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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> --
> Joe Jordan
> --
> Gromacs Users mailing list
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