When studying transitions between molecular states, a common challenge in computational chemistry is building a reliable minimum energy path connecting two conformations. This is essential for exploring reaction mechanisms, ligand unbinding, or protein conformational changes. But what’s the most efficient…
When working with coarse-grained (CG) molecular dynamics simulations, one common scenario is modeling systems that contain multiple copies—or replicas—of the same protein. This is typical in studies involving protein aggregation, crowding effects, or multi-component assemblies using approaches like the MARTINI…
When working with large molecular systems, identifying specific atoms with precision can be time-consuming and frustrating. Whether you’re cleaning up a model, extracting meaningful subsets, or analyzing specific substructures, selecting atoms by hand becomes inefficient and error-prone very quickly. This…
When working on complex molecular visualizations, clarity matters. Whether you’re analyzing large biomolecular systems or creating compelling visual outputs for presentations or publications, the choice of color can dramatically impact how easily your audience interprets molecular structures. One of the…
Energy minimization is a crucial preparatory step in molecular simulations, especially before launching longer production runs such as molecular dynamics (MD). A poorly minimized system may result in unstable simulations, wasted computational resources, and misleading scientific conclusions. Yet many modelers…
