Author: OneAngstrom

Molecular modelers often need more than static visualizations to communicate complex structural changes, docking processes, or dynamic behaviors. Animations and interactive presentations can significantly enhance clarity, whether you’re prepping material for a talk or sharing insights with a broader audience.…

When setting up molecular simulations, especially for solvated macromolecules, an often-overlooked yet crucial detail is the shape of the unit cell. If you’re a molecular modeler working with periodic boundary conditions (PBC), the choice of cell shape can make a…

Visualizing molecular docking is an essential part of many presentations in molecular modeling. Whether you’re showing how a ligand fits into a protein binding site, or preparing a video to share with collaborators or students, the process of creating smooth,…

When presenting molecular models, small visual tweaks can make a big difference. One of the common challenges for molecular modelers is helping audiences stay focused on the scientific message instead of being distracted by inconsistent or harsh visual transitions. That’s…

Edit a group of atoms confidently without breaking their internal structure? If you’re modeling or modifying molecular systems in SAMSON, this question is probably familiar. Precise control over atom positioning can be tricky, especially when you’re dealing with groups rather…

A frequent challenge in molecular modeling is clearly conveying how molecules interact—especially when it comes to docking. Static images can’t capture the nuances of molecular movement, and scripting animations manually can be time-consuming and unintuitive. If you’ve ever wanted a…

When designing synthetic or biopolymers, having precise control over the bond types between monomers is often critical — not just for chemical accuracy, but also for predicting properties like stability, flexibility, or conductivity in downstream simulations. SAMSON’s Polymer Builder extension…

When presenting molecular models, how you guide your audience’s attention can make the difference between understanding and confusion. In molecular animations, camera movement isn’t just about navigation—it’s about storytelling. Among the various features available in SAMSON, one that often gets…

Adapting molecular dynamics simulations to specific systems often requires precise control over simulation parameters. However, editing .mdp files manually or ensuring consistency across simulation steps—like energy minimization, NVT/NPT equilibrations, and production runs—can be time-consuming and error-prone. If you’re working with…