If you are running Minecraft as a service stop the service and then run this command to get into the Minecraft console

java -Xms512M -Xmx1008M -jar /home/user/minecraft/spigot-1.16.5.jar -nogui

Once the server has started you can give yourself operator status with the op command

/op *minecraftname*

You can then reboot to start the automatic service again if you have that setup

To configure your Minecraft server you will open the config file server.properties and change certain options from there