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: Average=1.004 Stdev=0.7661 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? Thanks, Soren Enemark
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