$root is a QC command available in all games. It resets what bone is used as the "root" bone if there are multiple root - no parent - bones. The root bone is used for all movement and rotation calculations, as well as setting the root bone for ragdolls. This command is usually used to remove controller bones from the animation process.
$root <bone name>
$modelname "npcs/dog.mdl" $cdmaterials "models/npcs/" $model "Dog" "dog.smd" $root "pelvis" $sequence "idle" "idle.smd"