[gmx-users] mean square displacement frequency

Yongchul Chung yxc169 at case.edu
Tue Jul 27 19:51:56 CEST 2010

Hello gmx-users,

I have trajectories which has been obtained from simulating 20,000 atoms in
NVT simulation for 25ns.  I recorded the trajectory every 3ps which means
that I have 60,000 data points per atom. I am trying to construct a
histogram where y-axis is the frequency (# of atoms) and x-axis is the mean
square displacement over 25ns.

I think a simple way to achieve this by looking at individual atoms and
calculate its msd over 25ns and put them in a bin. But there are 20,000
atoms there and 60,000 data points per atom which makes me hard to do this
on a spreadsheet -- even if I cut down the data points for each atoms by two
orders of magnitude, I have to deal with 12 million data points. My other
option is scripting... but I am trying to avoid this as much as possible at
this point.

To re-iterate my question, is there a built-in way to compute msd for each
atoms and put them in bins?

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