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

[David van der Spoel]

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.
________________________________________________________________________
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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