You cannot run a web service as root. You have to run the entire WEB CONTAINER as root. J2EE servers - or at least all the ones I've ever known - run all apps as the same OS user as the container itself, which in turn runs as whatever user the JVM started as. It would, in fact, be pretty difficult indeed in most JVMs for one VM instance to run under multiple OS user IDs.
However, before you unleash yet one more security menace on the Internet, perhaps you can describe what you need to run an application as root to begin with. We might be able to find a way to reduce the exposure.
An IDE is no substitute for an Intelligent Developer.