Molecular Dynamics Simulation of Two Toluene Molecules in Vacuum Using GROMACS
- Avighna Daruka
- Apr 6
- 1 min read
Prasha Maskey (1) (1) St. Xavier’s College, Loyola Campus — Kathmandu, Nepal
Toluene is an extensively used solvent for chemical synthesis and pharmaceutical production. In spite of its abundant use, the dynamics of its bimolecular interactions remain insufficiently characterised in scientific literature. In this study, GROMACS was employed to investigate collision dynamics between two molecules of toluene to identify energy exchange mechanisms. This draws a simple analogy to high-energy particle physics, specifically particle accelerators, where particles are accelerated to probe forceful collisions in order to understand energy exchange mechanisms. The simulation included energy minimisation, NVT equilibration and MD runs. The system reached the target temperature of 298 K and remained stable throughout the equilibration process. Analysis of distance graphs revealed that the centre-of-mass distance became stable at approximately 3.8 nm and the minimum atomic separation at about 3.2 nm, meaning under these specific experimental conditions, no direct collision occurs between two toluene molecules. These results demonstrate that toluene-toluene interactions exist in a dynamic equilibrium governed by van der Waals forces, and no stable aggregate is formed upon interaction.
Keywords: molecular dynamics simulation, GROMACS simulation, toluene-toluene interaction, van der Waals forces molecular simulation, computational chemistry
Article Type: Original Research
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Nice clear write up of a simple system. The finding that centre-of-mass distance stabilises around 3.8 nm with no direct collision is a useful negative result, and those are underpublished. One practical note for others rendering trajectories from GROMACS: I pull a still out of the MD run with a Video Thumbnail tool for slide decks rather than screenshotting the viewer. Would like to see this repeated at higher temperature.
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