[gmx-users] g_msd and MSD analysis

[Mr Bernard Ramos]

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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