The molecular dynamics simulations provide great details at the nanoscale level for relatively big systems (up to several million atoms). Very often the material environment of certain functional groups, selected atoms, clusters of atoms, and other low to high-level structural elements, is numerically evaluated employing radial distribution functions (RDF). That method is powerful, well studied, and largely implemented for analysis. But it cannot provide a visual spatial estimate for the investigated environment. If you have a molecule surrounded by ions, it is not easy to explain to the audience where the ions are concentrated in the simulation box and what kind of 3D structures they are involved in.

One way to overcome that problem with the visualisation is to use the ensemble average method. That method excludes the time from the generated molecular dynamics trajectory and plots the local measures of the probability mass function in 3D. The video presented below employs the methodology outlined in the Supporting Information article (see S6 there) for computing ensemble averages:

https://pubs.acs.org/doi/suppl/10.1021/acs.jpcb.5b06566/suppl_file/jp5b06566_si_001.pdf

The visualisation materials were computed on the Discoverer Petascale Supercomputer using the CPU-optimized GROMACS 2024.1 version available in the software repository.