[gmx-users] diffusion, g_msd and trestart

Enemark Soeren chees at nus.edu.sg
Mon Jul 27 11:05:44 CEST 2009

Dear all,

I am trying to calculate diffusion coefficients for a system of (30)
glycine molecules in a box with (1000) water.


After running:

g_msd -f md.xtc -s md.tpr -mol -n molindex.ndx


I get a list of diffusion coefficients - one for each glycine molecule.
I then calculate the average and the stdev:





My problem is that the stdev is very great! More than +/- 75% of the
average value.

Why is that?


Also, what is the reason for the trestart=10 default value? Shouldn't it
be better to have trestart=1, if my xtc file is saved every 1 ps?



Soren Enemark

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