In this paper, a new tool dedicated to the analysis and the conception of molecules is presented. It is composed of an adaptive simulation software and a haptic device used to interact with molecules while feeling either the forces applied by the environment or the internal forces. The adaptive articulated body algorithm allows fast simulations of complex flexible molecules. To handle the coupling with the force feedback device, two different control schemes designed for nanoscale applications and providing high transparency rendering are proposed and compared. The system we propose is highly flexible since either a single rigid body or the entire molecule can be manipulated via the haptic device. The user can choose between setting a desired position/orientation of the molecule, or apply forces/torques to manipulate it. It allows the operator to control each stage of the design process of new molecular structures. The validity of this tool is demonstrated through examples of haptic interaction between the HIV protease and its inhibitors, and unfolding one of these drugs.