[gmx-users] g_msd and pbc

[Chandan Choudhury]

Dear gmx_users,

I was just wondering how the g_msd (of gmx 4.0.7) code, takes care of the
PBC. e.g. If I want to calculate the lateral diffusion of a lipid bilayer
and at some point of the trajectory, some lipid molecules, due to PBC in
the lateral direction, might pop out from one side of the box and re-ener
from the other side. I such a situation it should show a very lage msd, but
actually in the g_msd code, this fact is taken care of. Can some one
explain, how is this effect taken care of.


Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
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