SMTP goes down daily for few minutes and how will it affect server performance?

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http://serverfault.com – Our web server will dispatch around 55,000 of alerts and they will be delivered in a batch of 500 by mail server. Our site behaves very slow in afternoon and it takes 6-8 minutes for admin to get logged in. Initially we thought that the fault is at processing the 55,000 alerts. But it took 30 min to process and it is OK. Mail server some times goes down because of full output. What may be the other issue why the response from server is slow. It is not problem with server location because other sites on same server run well. On looking into Munin (server monitoring tool) it shows that almos (HowTos)