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

[Chih-Ying Lin]

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.



Does g_msd remove the effect of 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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