Reinstall El Capitan Without Erasing the Drive
Make sure you have a current backup before proceeding.
Boot to the Recovery HD:
Restart the computer and after the chime press and hold down the COMMAND and R keys until the menu screen appears.
Repair
When the recovery menu appears select Disk Utility and press the Continue button. After Disk Utility loads select the indented Macintosh HD entry from the the left side list. Click on the First Aid tab in the toolbar.. If Disk Utility reports any errors that have been fixed, then re-run First Aid until no errors are reported. Wait until the operation completes, then quit Disk Utility and return to the main menu. Select Restart from the Apple menu.
Reinstall OS X: Select Reinstall OS X and click on the Continue button.
Note: You will need an active Internet connection. I suggest using Ethernet if possible because it is three times faster than wireless and more reliable.