When creating molecular animations, it’s common to focus on the dynamics of a specific region of a system — maybe a ligand binding site, an active pocket, or a flexible loop. However, one common frustration is keeping that region consistently…

If you’re working in molecular modeling, you’re probably used to sending around project files via email or generic cloud services. Whether you’re collaborating on a paper or running simulations with worldwide colleagues, this process can become chaotic fast: mismatched versions,…

Preparing a receptor for a molecular docking simulation can sometimes feel more complex than the docking itself. Whether you’re working on a protein-ligand system or trying to simulate docking into DNA or RNA, the setup process can be a source…

When working with complex molecular systems, you sometimes need to optimize just a portion of a molecule—such as a side chain, a loop, or a binding site—without disturbing the rest of the structure. Minimizing the entire molecule can lead to…

Mistakes happen 🧬. Whether you’re exploring a new protein conformation, editing a reaction intermediate, or simply rearranging atoms in your molecular design, it’s easy to misclick and lose a key step. Fortunately, SAMSON offers a dedicated History view feature that…

When working with complex molecular systems, modelers often need to isolate specific groups of atoms to perform targeted operations, run simulations, or build visualizations. One recurring task is selecting heavy atoms — that is, atoms that are not hydrogen. This…

When exploring molecular systems, molecular modelers often reach a turning point: they need to go beyond viewing and start editing atomistic properties. Whether for preparing simulations, constructing variants of a molecule, or cleaning up input data, changing a molecule’s internal…

When you’re designing molecular presentations, timing is everything. Whether you’re teaching, presenting to colleagues, or preparing a video abstract for a publication, manually toggling the visibility of molecular nodes can be time-consuming—and often results in jarring, unnatural transitions. This is…

When exploring molecular motions, one common challenge for modelers is how to effectively capture and reuse intermediate or final conformations. Whether you’re inspecting how a ligand access channel opens, or evaluating different configurations of a flexible loop, you often find…

When setting up a molecular system for simulation in GROMACS, atom group selections—known as index groups—play an important role in defining regions for restraints, analysis, and advanced sampling techniques like umbrella sampling. While GROMACS automatically generates standard index groups (e.g.,…