[gmx-users] coordinates file format

[Mark Abraham]

On Mon, Jan 26, 2015 at 5:31 PM, mah maz <mahmaz71 at gmail.com> wrote:

> Dear Mark,
>
> Thanks for your reply. I think it is not! I have 4000 atoms, the first
> number is time, then 4000 x y and z: x1,y1,z1, x2, y2, z2, ....,x4000,
> y4000, z4000. They are following each other not in a special order. Then
> the next time step starts with x1,y1,z1,....,x4000, y4000, z4000. So, they
> are not in a column as they are supposed to be.


What do you mean by "they?" Every atom has three adjacent columns and each
of the dimensions has its own column. Your example of a preferred format
did this also.


> Can I do anything to a
> result file to be in my preferable format?
>

The only difference in your preference seems to be extra whitespace between
triples of columns corresponding to atoms. This is basically unnecessary
for doing parsing - you already know that the columns are in triples of
xyz. You could insert the extra whitespace yourself with your scripting
language of choice, but the only advantage of that might be if you then
plan to read the format into a Fortran program, in which case you deserve
pain for not using libxdrfile to read the original trajectory ;-)

Cheers,

Mark


> Many Thanks!
> Regards,
> Mah
>
> On Mon, Jan 26, 2015 at 12:08 PM, mah maz <mahmaz71 at gmail.com> wrote:
>
> > Hi Mark,
> > I want to have X Y Z of each atom for all time step apart from other
> atoms
> > so that I can use them as data for programing; like this for instance:
> > t    x1 y1 z1          x2  y2  z2
> > 0    2.4 3.5 4.5       5.6 7.9 9.8
> > 0.1  5.5 6.7 8.9
> > ...
> > in which 0 and 0.1 are time and the rest are x1 y1 z1 of the 1st atom and
> > x2 y2 z2 are for the 2nd atom.
> > Is it possible to get the file in a desired format?
> > thank you!
> >
> > On Mon, Jan 26, 2015 at 11:54 AM, mah maz <mahmaz71 at gmail.com> wrote:
> >
> >> Dear all,
> >>
> >> I have extracted a file of coordinates after a simulation with 1000000
> >> steps writen every 1000 steps, by "g_traj -s -ox" . The result is a
> file in
> >> which the first column is time and all coordinates are following it. Is
> >> there a way that I can get coordinates of each time step in a more
> >> classified way?
> >>
> >> Thanks!
> >>
> >
> >
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