[gmx-users] Diffusion beyond periodic boundary

Tsjerk Wassenaar tsjerkw at gmail.com
Sat Feb 9 09:24:23 CET 2013

Hi Kenji,

You can remove the jumps/rewinds using 'trjconv -pbc nojump'.



On Sat, Feb 9, 2013 at 4:45 AM, Kenji Mochizuki <kmochi at ims.ac.jp> wrote:

> 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
> Kenji
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4

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