[gmx-users] Diffusion beyond periodic boundary
kmochi at ims.ac.jp
Sat Feb 9 04:45:00 CET 2013
I have performed MD run with periodic boundary condition,
which system is consist of water and LJ particles.
I would like to know the time dependence of the dislocated distance (diffusion) from the starting time (t=0).
Firstly, I made pdb file of the trajectory, then calculated the distance from pdb file.
However, when the particle goes beyond periodic boundary,
the x-y-z coordination is rewind into the box size.
So, the dislocated distance is wrong.
Could you please tell me how to calculate the dislocated distance accurately ?
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