Devices, systems, and methods for avoiding collisions between manipulator arms using a null-space are provided. In one aspect, the system calculates an avoidance movement using a relationship between reference geometries of the multiple manipulators to maintain separation between reference geometries. In certain embodiments, the system determines a relative state between adjacent reference geometries, determines an avoidance vector between reference geometries, and calculates an avoidance movement of one or more manipulators within a null-space of the Jacobian based on the relative state and avoidance vector. The joints may be driven according to the calculated avoidance movement while maintaining a desired state of the end effector or a remote center location about which an instrument shaft pivots and may be concurrently driven according to an end effector displacing movement within a null-perpendicular-space of the Jacobian so as to effect a desired movement of the end effector or remote center.
