[gmx-users] coordinates file format

[mah maz]

Dear Mark,

That was a great deal of help. This time, I agree with your last sentence
;-) Thanks a lot!

Cheers,
Mah

On Wed, Jan 28, 2015 at 2:23 PM, mah maz <mahmaz71 at gmail.com> wrote:

> 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!
>>>>>
>>>>
>>>>
>>>
>>
>