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

[Justin A. Lemkul]

Chih-Ying Lin wrote:
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> 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.
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> Does g_msd remove the effect of the periodic boundary condition ?

Yes.

> 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

No need.  See above.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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