[gmx-users] coordinates file format

[mah maz]

Dear Mark, Erik

Mark, thank you very much! I asked google and it didn't know either! ;-)
your code also didn't work in FORTRAN. I've searched and found out it is
not probably an easy task to read a .trr file and even .xtc in FORTRAN.
Have you got any other ideas?
Erik, It took me more than 5hrs to read it in FORTRAN and I couldn't
succeed! I'm not familiar with python. thanks anyway.
Regards,
Mah

On Tue, Jan 27, 2015 at 12:31 PM, 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?
>
> 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!
>
> 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!
>
> 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!
>>>>
>>>
>>>
>>
>