[gmx-users] Diffusion beyond periodic boundary

Kenji Mochizuki kmochi at ims.ac.jp
Sat Feb 9 04:45:00 CET 2013

Dear All

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 ? 

Best regards


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