Author: OneAngstrom

Running molecular dynamics (MD) simulations across multiple systems can be one of the most time-consuming bottlenecks in molecular modeling. If you’ve ever found yourself repeating the same preparation and simulation steps manually for dozens of protein-ligand systems, you likely know…

Many molecular modelers know the frustration: you load a ligand or protein into your modeling environment and need to align it properly in 3D space—maybe for comparison, maybe for analysis, or maybe just to organize a complex scene. But trying…

A common challenge in molecular modeling is the need to make small, precise changes to a structure without affecting the overall geometry. Whether you’re adjusting a functional group, refining a ligand conformation, or modifying only part of a large system,…

Researchers working with molecular dynamics simulations often need to rely on specific configuration files to fine-tune the behavior of simulation engines like GROMACS. Among these configurations, the .mdp file (Molecular Dynamics Parameters file) plays a central role. However, editing or…

Most molecular modeling begins with the ideal. Perfect lattices, flawless symmetry, and pristine atomic arrangements. But real-world materials are rarely so tidy. Defects — like vacancies, substitutions, and distortions — play a crucial role in defining the physical and chemical…

When presenting complex molecular systems, timing matters. Animations that move too quickly from one state to another can overwhelm viewers, especially when trying to highlight an important molecular interaction or structural change. If you’re creating a molecular animation in SAMSON…

Running molecular dynamics simulations across a large number of protein structures—whether they are variants, mutants, or alternative binding poses—can quickly become overwhelming. Repeating the same MD preparation steps for each conformation or each structure wastes time, increases chances of human…

Creating clear, engaging molecular animations can be a challenge, especially when you want to highlight key transitions without overwhelming your audience with too much happening on screen. One common issue faced by molecular modelers and presenters is how to make…

Molecular modelers often face an underappreciated challenge: keeping track of numerous molecules, scripts, conformations, and structure files within a growing project. As the complexity of a molecular simulation increases, so does the burden of managing its components. A cluttered workspace…