[gmx-users] mean square displacement frequency
tsjerkw at gmail.com
Wed Jul 28 12:17:43 CEST 2010
So you want a distribution of MSD, right?
> 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.
25000/3 = 8333
Where do these 60k per atom come from?
>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.
g_rmsf gives you sqrt(MSD) per atom. That should bring you quite close
to what you need.
Also give the manual a read once (more); there's many more tools that
can do all kinds of things that may at some point be useful.
Tsjerk A. Wassenaar, Ph.D.
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
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