[gmx-users] negative diffusion constant by g_msd -mol option

David van der Spoel spoel at xray.bmc.uu.se
Thu Jan 11 09:13:42 CET 2007

m-hatake at jaist.ac.jp wrote:
> Hello all,
> I calculate diffusion constant for each individual molecule
> using g_msd and -mol option.
> There are some negative values in the output file.
> Diffusion constant is always positive value, isn't it?
> I don't know how negative value is calculated.
> I am using gromacs 3.2.1.
> give me some advice, please.
This is because the statistics for a single molecule is poor. One 
molecule may start by a fast movement in one direction, and then slowly 
drift back. In the case the slope of a fit to the MSD will be negative.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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://folding.bmc.uu.se

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