I use the program SMOG: Structure-based Models for Biomolecules for this. The benefit of performing molecular simulations in reduced units is the simplification of calculations, which can be especially useful for complex systems like DNA or proteins with many different types of atoms. In reduced units, variables like energy, temperature, pressure, and distance are rescaled to dimensionless values based on characteristic parameters of the system (such as interaction energy and distance). This makes it easier to compare different simulations, regardless of the exact physical properties of the atoms involved.
For large molecules like proteins or DNA, which have many atoms with varying masses and interactions, using reduced units allows you to treat all these atoms in a more generic way, without needing to account for the specific physical constants of each atom type. This can speed up the calculations, making the process more efficient, and allows for clearer analysis of the system's behavior patterns.
Using reduced units in molecular dynamics (MD) simulations simplifies calculations by making properties dimensionless, allowing for easier comparison across systems. It is particularly useful for studying fundamental physical behaviors without being tied to specific units. However, for complex biomolecules like DNA or proteins, reduced units may oversimplify interactions, making them less practical for detailed biological simulations.
All of which can be easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.