for a big database you should either remove the database from the disk (after you stop the engine first I guess) or use in Cypher something like:
MATCH (n)
OPTIONAL MATCH (n)-[r]-()
WITH n,r LIMIT 50000
DELETE n,r
RETURN count(n) as deletedNodesCount
see https://zoomicon.wordpress.com/2015/04/18/howto-delete-all-nodes-and-relationships-from-neo4j-graph-database/ for some more info I've gathered on this from various answers