Enemark Soeren wrote:
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?
Short simulation most likely. Since these things are big it takes a long
time to equilibrate.
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?
No, because there is correlation in the system. Ideally you would take
this time to be longer than the correlation time. You could try to find
an estimate of that from the velocity autocorrelation.
Thanks,
Soren Enemark
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