I am running an application on linux machine. By giving the ip address of a windows machine as input, the application must shutdown the windows machine. If the machines run
You need a way to launch a shell on the Windows box so you can run th shutdown command built in to Windows.
You can install Cygwin for this, then install an SSH daemon in Windows. Once that's running, your Linux box can run commands on the Windows box just as if it were another Linux machine.
Here are some instructions for setting up Cygwin's sshd in Windows.