I am setting an alert based on the count i.e if the count is greater than 50 then we need to generate an alert.
I wrote the query and saved as alert
alert type=Real time
Custom Condition= search count>50
time: in 5 mins
and then selected the e-mail as triggered condition
in Throttle what should I give such that the alert when generated in 5 minutes should set the time back to zero before generating another alert
If your search is scheduled to run every five minutes (is it, actually?), then set the throttling to suppress the alert to something greater than five minutes.
I think it might be helpful to reconsider the alerting behavior you would like to have. When you say, "set the time back to zero" in your original question, it makes me think that you might want a scheduled alert that runs a search every five minutes to check for more than 50 events. If there are more than 50 results for that search, you get an email notification. Does that sound more like the outcome you are trying to set up? Let me know either way and I can suggest some resources.
As a start, this comparison chart might help.