Hi everyone!
I have a 20 ns simulation (2fs timestep but coordinates saved every 0.2 ps)
and I was able to calculate the mean-square-displacement of the oxygen atoms of
my water solvent. The entire MSD plot looks very linear to me. I need to fit
this set of MSD data to obtain the diffusion coefficient. However, I am not
sure if I will have to use the entire MSD points or may be just to consider a
few picoseconds at the latter part of the simulation time. In papers I have
read, they use up to a 100 ps, although no mention were made as to where those
set of points came from. Please help.
This post seems to suggest a nanosecond window for the analysis of the MSD curve
http://lists.gromacs.org/pipermail/gmx-users/2012-January/067487.html
Although, this other one suggests using the latter 40 ps of his MSD
http://lists.gromacs.org/pipermail/gmx-users/2009-November/046990.html
Your help is greatly appreciated.
Thanks,
Bernard
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