AMBER Archive (2009)

Subject: [AMBER] The MSD and periodic boundary condition

From: Chih-Ying Lin (chihying_at_usc.edu)
Date: Thu Nov 19 2009 - 17:30:46 CST

Hi
With the periodic boundary condition, all the recorded coordinates of the atom are within the simulation box.
To calculate the MSD, the movement of the center mass of the molecules between this time step with the next time step is calculated without considering the periodic boundary condition.

But all the recorded coordinates of the atom are within the simulation box after considering the periodic boundary condition.
So, how can I remove the periodic boundary condition to get the truly movement of the atoms between the two time steps ?

Thank you
Lin

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