Question: how to set ntp server on windows 2008 r2 domain controller?
Answer: Open the command prompt and type: net stop w32time.
Configure the external time sources, type: w32tm /config /syncfromflags:manual /manualpeerlist:0.pool.ntp.org.
Make your PDC a reliable time source for the clients. ... 
Start the w32time service: net start w32time.