From: RonitS Chem (
Date: Thu Oct 22 2020 - 13:09:34 CDT

Hello all,

I want to calculate the diffusion constant for a number of water models and
so need to calculate the MSD from the 2ns trajectories I have. I am using
my own python code, but I realize that since the periodic boundary
condition is under effect I cannot calculate the distances properly.

Since I use VMD to print out the snapshots for MSD calculations, is there
any way to account for PBC? I would like to get rid of it, in other words
get the unfolded coordinates for the atoms but I do not know how to do it.
Any help or insight would be much appreciated.

I have seen the RMSD tool in VMD but when I calculate the RMSD and square
it to get the MSD, it is not a straight line as expected. I assume this is
because of the PBC as well. I am fairly new to all this, so please forgive
me if I am missing something simple.