[gmx-users] coordinates file format

Justin Lemkul jalemkul at vt.edu
Mon Jan 26 17:34:33 CET 2015

On 1/26/15 11:31 AM, mah maz 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?

Which sort of format would you prefer?  You say the coordinates are not in a 
"special format," but in fact they are in a completely predictable format, which 
you have identified - (x,y,z) for every atom in the selection.  The output is 
indeed cumbersome (it is a bit of a number dump), but it is easily parsed with 
any scripting language because the order is known.  The file may not be 
aesthetically pleasing, but it's perfectly functional.


> 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!


Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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