[gmx-users] coordinates file format

mah maz mahmaz71 at gmail.com
Tue Jan 27 10:01:58 CET 2015

Dear Justin and Mark,

I think you are both right.

I didn't get your last sentence Mark! What is a libxdrfile?

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
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!

According to your points, I can come to the conclusion that changing the
file format is not possible.
I appreciate your help as usual. thanks alot!


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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