[gmx-users] coordinates file format

mah maz mahmaz71 at gmail.com
Mon Jan 26 17:31:16 CET 2015

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

Many Thanks!

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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