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? Greg
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