[gmx-users] coordinates file format

[Mark Abraham]

On Tue, Jan 27, 2015 at 10:01 AM, mah maz <mahmaz71 at gmail.com> wrote:

> Dear Justin and Mark,
>
> I think you are both right.
>
> I didn't get your last sentence Mark! What is a libxdrfile?
>

Ask google ;-) It's a library distributed from the GROMACS website to make
it easier to read files into C and (particularly) Fortran programs.


> Justin, The problem is I have so many atoms in the system. As I said the
> best format for reading data is to be like this:
> time     x1 y1 z1     x2 y2 z2   ....... xn yn zn
> 0          1 2 3           2 3 4               8 5 6
> 0.1
> 0.2
> ...
> as you know the trajectory format is like this:
>
> (t=)0      x1 y1 z1  x2 y2 z2   x3 y3 z3  x4 y4 z4.......
> x5 y5 z5   ......... x4000 y4000 z4000
> (t=)0.1   x1 y1 z1  x2 y2 z2..............
> x5 y5 z5  ....... x4000 y4000 z40000
> completely difficult and confusing for me and the program both!
>

The following pseudocode reads both, because they're the same thing!

ignore_useless_title_row_if_present()
for frame (1 .. end of file)
  frametime[frame] = read_next_number()
  for atom (1 .. number_of_atoms)
    for dim (x y z)
       framecoords[atom][dim] = read_next_number()

The field widths are fixed, so this probably even works in Fortran.

According to your points, I can come to the conclusion that changing the
> file format is not possible.
>

It's perfectly possible to write a script to transform it to whatever you
like. But that would serve no useful purpose.

Mark


> I appreciate your help as usual. thanks alot!
>
> Cheers,
> Mah
>
>
>
>
>
>
>
> On Mon, Jan 26, 2015 at 8:01 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. Can I do anything to a
> > result file to be in my preferable format?
> >
> > 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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