[gmx-users] coordinates file format
mahmaz71 at gmail.com
Wed Jan 28 11:53:52 CET 2015
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.
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
> 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!
>> 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?
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