how to run a command at terminal from java program?

You need to run it using bash executable like this:

Runtime.getRuntime().exec("/bin/bash -c your_command");

Update:
As suggested by xav, it is advisable to use ProcessBuilder instead:

String[] args = new String[] {"/bin/bash", "-c", "your_command", "with", "args"};
Process proc = new ProcessBuilder(args).start();