Model verification is a critical aspect of scientific accountability, transparency, and learning. Here, we demonstrate an application of a model verification approach for a molecular dynamics (MD) simulation, where the interactions between silica and silk protein were studied experimentally toward understanding biomineralization. Following the ten rules for credible modeling and simulation of biosciences as developed in Erdemir et al., the authors of the original paper collaborated with an external modeling group to verify the key findings of their original simulation model and to document this verification approach. The process resulted in successful replication of the key findings of the original model. Beyond verification, study of the model from a new perspective generated new insight into the basic assumptions. We discuss key learnings for how model validation processes can be improved more generally, specifically through improved documentation methods. We anticipate that this application of our protocol for model verification can be further replicated and improved to verify and validate other simulations.
Keywords: Interagency Modeling and Analysis Group; Model validation; Model verification; Molecular dynamics; Reproducibility.