Laboratories involving the construction of ternary phase diagrams are a staple of the physical chemistry undergraduate laboratory curriculum at many institutions. Here is highlighted an effort to enhance this type of laboratory experience with molecular dynamics (MD) simulations. Within this module of the lab students construct, run, and analyze MD systems involving a simple alkane, an alcohol, and water with the CHARMM forcefield in the GROMACS MD software package. Initial topologies (random insertion or layered) can be constructed using GROMACS built-in or web-based tools, such as the CHARMM-GUI. Common issues that can arise when introducing MD simulations in an undergraduate lab setting are discussed.

Enhancing the physical chemistry laboratory with molecular dynamics simulations: Ternary phase diagrams

ACS Spring 2022

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