Author: OneAngstrom

When preparing a coarse-grained (CG) molecular system, especially using the MARTINI force field, it’s easy to overlook a small yet critical detail that can impact your entire simulation: the default van der Waals (vdW) distance used during solvation. This post…

When creating molecular presentations or simulations, one of the biggest challenges scientists face is guiding the viewer’s attention to specific events. Sometimes, molecules are added or removed, or key regions switch configurations. These changes are important but can easily get…

Energy minimization is a key step in the molecular dynamics workflow. It helps to remove steric clashes or geometric problems in your molecular model before moving on to more computationally intensive stages like equilibration and production runs. But after clicking…

When preparing molecular animations to communicate modeling results, clarity and visual progression are key. Whether you’re recording a molecular dynamics simulation or simply creating a narrated presentation for a classroom or conference, transitions help guide viewers’ attention. One transition that’s…

Communicating molecular mechanisms clearly is a recurring challenge for molecular modelers, especially when presenting ligand-receptor interactions, docking pathways, or structural transitions. One simple but often overlooked pain point is illustrating how a ligand undocks from its receptor. This step is…

Staring at molecular structures for hours can be demanding, especially when working late or in low-light environments. If you’ve ever found yourself squinting at a brightly-lit interface while modeling proteins, docking ligands, or adjusting rendering settings, you’re not alone. Dark…

When setting up coarse-grained (CG) systems for molecular dynamics simulations with GROMACS, one common source of instability and frustration is poor solvation—especially when solvent molecules are placed too close to solute atoms, causing steric clashes. Fortunately, SAMSON’s GROMACS Wizard offers…

Visualizing molecular systems effectively is one of the key challenges faced by scientists, researchers, and educators working in structural biology, drug design, and materials science. Molecules are complex, and meaningful insights often depend on being able to visualize relevant structures…