Combined-resolution simulations are an effective way to study molecular properties across a range of length and time scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size and/or shape) as the simulation progresses. The number of degrees of freedom required to accurately represent even a simple molecular process can vary by several orders of magnitude throughout the course of a simulation, and adaptive boundaries react to these changes to include an appropriate but not excessive amount of detail. Here, we derive the Hamiltonian and distribution function for such a molecular simulation. We also design an algorithm that can efficiently sample the boundary as a new coordinate of the system. We apply this framework to a mixed explicit/continuum simulation of a peptide in solvent. We use this example to discuss the conditions necessary for a successful implementation of adaptive boundaries that is both efficient and accurate in reproducing molecular properties.