[gmx-users] coordinates file format

Erik Marklund erik.marklund at chem.ox.ac.uk
Tue Jan 27 10:23:32 CET 2015

On 27 Jan 2015, at 09:01, mah maz <mahmaz71 at gmail.com<mailto:mahmaz71 at gmail.com>> wrote:

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!

So if I get this right you want to change the spacing between xn yn zn and xn+1 yn+1 zn+1. It will take you 5 min to write a python script to do that. And I can’t see why the current output format would be “confusing” for a program.

Kind regards,

Erik Marklund, PhD
Postdoctoral Research Fellow, Fulford JRF

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road

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