[gmx-users] mean square displacement frequency
yxc169 at case.edu
Wed Jul 28 19:08:43 CEST 2010
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.
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
> > 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
> > 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
> > on a spreadsheet -- even if I cut down the data points for each atoms by
> > 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.
> post-doctoral researcher
> Molecular Dynamics Group
> Groningen Institute for Biomolecular Research and Biotechnology
> University of Groningen
> The Netherlands
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