We have a MySQL server in one of the remote Virtual Machine (Windows Server 2008). Till yesterday we were able to connect to the MySQL server, with the help of workbench install
On MySQL v5.6 this may be the case. When another server communicate by advertising its hostname instead of IP address, the resolution might fails (because your user is using IP address instead of hostname for example).
So, you need to disable the following,
skip-host-cache
skip-name-resolve
Or maybe create the user with appropriate hostname (instead of IP address). You may find the hostname when establishing the connection to the remote MySQL.