[gmx-users] mean square displacement frequency

[Yongchul Chung]

Thanks -- I actually find out a way to do this. Just extract coordinate
information from trajectory file in pdb (for my case, 0ps and 25ns) and
compute displacement by yourself.

Greg

On Wed, Jul 28, 2010 at 6:17 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Greg,
>
> 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.
>
> Cheers,
>
> Tsjerk
>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> Groningen Institute for Biomolecular Research and Biotechnology
> University of Groningen
> The Netherlands
> --
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