[gmx-users] g_msd and pbc
spoel at xray.bmc.uu.se
Wed May 14 21:40:01 CEST 2003
On Wed, 2003-05-14 at 19:09, emombel at nimr.mrc.ac.uk wrote:
> I am about to compute MSDs for a lipid bilayer. I was wondering how the
> periodic boundary conditions are handled by the program g_msd.
> Could anybody be of some help?
It tracks between from frame to frame what is the shortest displacement,
so if you do the analysis with a 2 nm box you will see that your MSD can
be much more than the size of the box (squared) if you simulate long
> Enrico Mombelli
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Dr. David van der Spoel, Dept. of Cell and Molecular Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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