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.
-Justin
Many Thanks!
Regards,
Mah
On Mon, Jan 26, 2015 at 12:08 PM, mah maz <mahma...@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 <mahma...@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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