to check if the periodic box was the correct size during simulation. It turned out that for the protein from BoHV-1 the box was the ideal size and the distances between periodic images were always higher than 21Å (Figure ), while, for the HSV-1 the periodic box was a bit too tight with several distances about 10Å (Figure ). However, for all three trajectories of HSV-1, there were only 3 snapshots recorded in one of the trajectories (0.01% of all recorded snapshots) where the protein residues were too close (below cutoff for long distance interactions of 9Å), which should not impact the results.