[gmx-users] coordinates file format

[Mark Abraham]

On Mon, Jan 26, 2015 at 9:38 AM, 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?
>

I don't understand. That is already the format of gmx traj -ox. You can see
that in the XVG legend. Re-grouping by atom number is straightforward to do
while you read it into whatever you plan to use next.

Mark


> 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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