The dynamics of systems of systems often involve complex interactions among the individual systems, making the implications of design choices challenging to predict. Design features in such systems may trigger unexpected behaviors or result in large variations in safety, performance or resilience. To provide a means of simulating such systems for aiding in these decisions, we have developed a prototype tool, the control-oriented dynamic computational modeling tool (CDCM). The CDCM provides rapid simulation capabilities to perform trade studies in systems of systems. The general class of systems of systems that we aim to examine involve multiple hazards, damage, cascading consequences, repair and recovery. We especially focus on systems-of-systems that incorporate a health management system (HMS) that can monitor the state of the habitat and make decisions about actions to take. In this paper we describe the features of the CDCM, the architecture we devised for simulation of systems-of-systems, the unique functionalities of this tool, and we provide a demonstration of the capabilities by performing two illustrative examples. We articulate the use of this tool for making early design decisions and demonstrate its use for trade studies that consider a model of a deep space habitat. We also share some experiences and lessons that may be useful for others seeking to address similar problems.