Have you been using screen like a n00b? Or worse, a service file that just starts screen?

Stop that nonsense and use a proper systemd service file instead!

This service file requires you to install mcrcon which you can obtain here: https://github.com/Tiiffi/mcrcon

You will have to set an rcon password (and enable RCON) in your Minecraft server.properties and then adjust the service file accordingly.

Set up RCON first as stated above and then:

useradd -d /var/lib/minecraft -m -r -s /usr/sbin/nologin minecraft

touch /etc/default/minecraft
chmod 0600 /etc/default/minecraft
cat <<EOF | sudo tee /etc/default/minecraft > /dev/null
RCON_PASSWORD=changeme
EOF

Modify /etc/default/minecraft so that RCON_PASSWORD is your actual RCON password.

Modify minecraft-vanilla.service (if needed) so that WorkingDirectory points to the directory with your minecraft's server.jar

Modify minecraft-vanilla.service (if needed) so that User and Group match the user and group you want to run the server as.

Modify minecraft-vanilla.service (if needed) so that the port of the RCON server in the ExecStop and ExecReload lines matches your RCON server port. Usually not needed if only running one Minecraft server.

Then install the service file with:

sudo install -o root -g root -m 0644 minecraft-vanilla.service /etc/systemd/system/minecraft-vanilla.service
sudo systemctl daemon-reload
sudo systemctl enable minecraft-vanilla.service
sudo systemctl start minecraft-vanilla.service

Simply run

sudo systemctl stop minecraft-vanilla
sudo systemctl disable minecraft-vanilla
sudo rm /etc/systemd/system/minecraft-vanilla.service
sudo systemctl reload-daemon

This service file is meant to be used with Minecraft vanilla.

If you are using Spigot, you must use minecraft-spigot.service instead.