For a web application, the JVM properties indeed need to be set for the application server's JVM and as such it cannot be set in the IDE. (The IDE cannot pass the parameters anyway since it merely invokes the commands provided by the appserver to start/stop/deploy-apps).
To solve your problem, you will need to set the JVM arguments at the appserver. You can set the JVM arguments in the admin console of the appserver. If you jush wish to set some environment properties for a given webapp, then you can use 'System.setProperty("environment.setting","local");' in the app's initialization code.