EC2 is not designed for database specifically
You seem to be installing and running your database on EC2 (what you call a linux AWS box
), this means you can SSH into the instance and install software manually and carry out updates and edit configuration files and settings etc.
RDS is designed for Database
RDS also has other really convenient features like automatic version upgrade and maintenance window management.
If your situation allows I would suggest to use a tool designed for database instead of having to configure things manually. It will save you a lot of time and troubleshooting, it is also more secured.
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