To set JAVA_OPTS options which you want to set additionally while running the tomcat should be set inside <tomcat home>/bin/setenv.sh if this file is not present then create one and set variable JAVA_OPTS="-Dsomething $JAVA_OPTS". If you have to set some variables while only starting the tomcat then you need to set those variables to CATALINA_OPTS rather than JAVA_OPTS.