From the command line, the two main reasons for not being able to run an executable are:
1) you don't have parmission. You've set things to give you permission, so this reason doesn't apply.
2) the path to the executable is not in your PATH environment variable. To see what's in path, run echo $PATH. I'll wager that you don't see the path to the external drive and the executable on that drive.
./Sim means 'in this directory, run this command'. In order for ./Sim to work, you need to first cd to the folder on the external drive which contains the executable, then do ./Sim.
Alternatively, you can run it as '/path/to/external drive/folder/executable'.
Third alternative is to add the path to that executable to your PATH variable.