Molecular Dynamics: A Tool for Undergraduate Engineering Students to Transform Their Understanding of Chemistry at Molecular Level

Molecular dynamics is a valuable tool in the field of chemistry that can be introduced as part of curriculum for engineering students at undergraduate (UG) level for better understanding of chemistry. Particularly engineering UG students have difficulty in understanding chemistry in terms of the molecular structures. Newtonian mechanics on the other hand is easily understood by the students pursuing engineering. Molecular dynamics, the branch of computational chemistry therefore can help these students to understand chemistry better if students also interpret the data and images produced by MD simulation. This case study describes the use of GROMACS, an open source code and visualizing packages like CHIMERA and VMD as a tool to perform MD simulations, which successfully reformed the approach of undergraduate students towards chemistry. The Molecular dynamics workshop was conducted for undergraduate students during summer vacation of 2015 to emphasize on conceptual understanding of chemistry and physics, using real life examples of mass transfer of compounds from one phase to another phase. This exercise encouraged the participating students to initiate their own learning in the field of molecular modeling.