AppDynamics works just as well with applications running outside of an application servers or container.

To install the agent on a standalone JVM, pass the path to the Java Agent when running the Java application in the following form:

java -javaagent:"/<agent_home>/javaagent.jar" <classname>

Ensure to add the -javaagent argument before the -jar argument. The javaagent argument value must reference the full path to the Java Agent home directory, including the drive on Windows. The classname should be the fully qualified class name with main method. 

For example, the following is an example of the command on Windows systems: 

java -javaagent:"C:\AppDynamics\agentDir\javaagent.jar"  com.main.HelloWorld

On Linux, it would be: 

java -javaagent:"/mnt/AppDynamics/agentDir/javaagent.jar" com.main.HelloWorld