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I ran vagrant init/up as root initially with one of my boxes, however, all of my other boxes are owned by a normal user, so every time I want to use the box as a regular user, I have to sudo and then change the key ownership to login.

I have changed all of the permissions in ~/.vagrant.d/*, and the vagrant files themselves. How can I access this box as non-root user? Is there another place I need to change permissions?

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Changing (or setting) the config.ssh.username = "vagrant" line in your Vagrantfile will allow you to ssh into another user account assuming it exists. You can also use `vagrant ssh -p' which allows you to manually enter the authentication credentials you would like to use each time you ssh into the box.

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