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Many engines have a setting called Move overhead. I even read about a formula that it should be set at x/150+y/3, where x is the base time and y is the increment.
But what does this parameter do? Is it a value by which the engine thinks it has less time than shown on the clock? For the whole game? Or for each move?
Does it depend on the GUI used? I usually set this at 100 for Arena but I use less for Fritz or Shredder. Not that I know why I exactly do this. How much does it affect performance?

Move overhead is to avoid losing on time in case played through network. Network matches induce ping.

Move overhead ("Overhead ms" in Komodo) is not just for internet play; even for games played on one machine some overhead is needed, but a much larger amount is needed for internet play. Unfortunately the definition and usage vary from engine to engine, and also depend on GUI and 0/S. For Komodo the default value should be high enough for play on one machine, but is not enough for internet games with lag. If you reduce the value, at least on Little Blitzer you will start to get time forfeits in fast games even on one machine. We have found that the default (50) can safely be reduced in Linux, at least on our own tester. We don't advise adjusting it based on the time control.

Thank you for the replies.

I would recommend always using it at the default setting, when doing CCRL-type testing. Engines are supposed to be aware that even under ideal circumstances (same machine and no load on it because of a pondering opponent) some lag will occur. If this makes them lose on time, it is a broken engine, even if it can be 'fixed' by increasing the lag option. An engine that has a broken default value is still a broken engine!