[gmx-users] coordinates file format
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.
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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