All viruses are protected by a durable protein shell regulating many crucial functions, such as host-cell infiltration and replication. Some disinfectants operate to disrupt or destroy this shell, rendering the virus inactive. However, many widely used antiviral solutions are also harmful to the environment and over prolonged usage, can be toxic to people or other desired organisms. Especially within enclosed environments, safer alternatives are necessary. This manuscript investigates the mechanisms behind CAGE, an ionic liquid that was previously identified to demonstrate antimicrobial properties and its interactions with a viral capsid protein. To do this, molecular dynamics simulations were used to simulate interactions between all the atoms involved in this process. Molecular dynamics simulations are a type of atomic-scale simulation based on computationally solving Newton’s laws of motion. The results showed that, on average, CAGE promotes certain forms of protein structure in regions of the viral protein vital for function, suggesting a mechanism for possible antimicrobial effects.