[gmx-users] periodicity in msd calculation

Bala subramanian bala.biophysics at gmail.com
Tue Aug 21 16:01:38 CEST 2012

I have calculate the mean sq. displacement of water molecules in the first
hydration shell around the protein (distance of .25nm). I want to write the
code but i dnt know how to manipulate the coordinates to account for the
pbc. Any guidance from anyone would be a great help.

Thanks in advance,
C. Balasubramanian

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