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We need a high precision (1ms) clock synchronization across multiple machines which are part of the domain. The idea is to use a PTP solution.

Is it possible to setup a computer which is part of the domain to use a different time synchronization mechanism? Would domain clock synchronization not interfere with it? Can it be disabled if so?

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Try just stop default Windows Time synchronization service and use Your own. It Ok as long as time in sync with domain in 5 min window.

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Windows supports synching time with non-domain servers. Just be aware that if the time interferes radically with the domain time, kerberos tickets will stop working and shares/printers/etc. will start to fail.

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