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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
