[gmx-users] g_msd => The MSD and periodic boundary condition

Omer Markovitch omermar at gmail.com
Tue Nov 24 13:09:50 CET 2009

On Fri, Nov 20, 2009 at 01:32, Chih-Ying Lin <chihying2008 at gmail.com> wrote:

> So, how can I remove the periodic boundary condition to get the truly
> movement of the atoms between the two time steps ?

Removing PBC and placing atoms back into their "true" location is easy. In
general, if an atom has moved more than half of the box between two
consecutive timesteps then it has "jumped" over the box.
You can see for example eq. 19 & 20 in doi:10.1063/1.2968608 .
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