I ran exactly same scripts on different machines (windows and linux).
Windows has one of the 2016 versions of LAMMPS and Linux has the latest
version. Simulations are TIP5P pure water models with Green-Kubo
algorithm (EMD). They have similar results when I run TIP3P models, but
with TIP5P, Linux machine overestimates the experimental result, while
Windows' results are in good agreement with the experiment. Both
machines are operating properly and have no observable problems (We use
them a lot in our research and this is the only type of simulation they
disagree with each other).