When simulating molecular mechanisms, such as how a ligand unbinds from a protein, researchers often face a specific challenge: known initial and final states of a system are available, but the energetically plausible path that connects them is not. This…

Creating accurate carbon nanotube (CNT) models is a common yet often cumbersome task in molecular design and nanoscience. Whether you’re preparing nanostructures for simulation or designing nanoscale devices, defining geometry and chirality vectors manually can interrupt your workflow. But what…

When working on molecular presentations, particularly those involving systems like membranes, surfaces, or long assemblies (e.g., DNA or polymer chains), it’s often essential to maintain a consistent perspective while shifting the viewpoint across the structure. A common challenge arises: how…

When you’re preparing a molecular presentation, timing can make a big difference. Whether you’re explaining a protein-ligand interaction to colleagues, teaching a structural biology class, or preparing a video abstract for your next paper—how and when your molecules appear on-screen…

For molecular modelers, quickly drafting, editing, and visualizing molecules often requires switching between tools—or between 2D and 3D views. This can lead to inconsistencies and disrupt the workflow. SAMSON’s Interaction Designer addresses this pain with a synchronized 2D-3D sketching environment…

Animating molecular structures is often a surprisingly repetitive task. If you’re a molecular modeler regularly preparing presentations or educational material, you probably spend far more time than you’d like moving atoms and tweaking their positions across frames. But building clean,…

When working with Protein Data Bank (PDB) files, molecular modelers often face a limitation: the structures frequently describe only asymmetric units—just a part of the full biological or crystal assembly. This can make it hard to visualize or simulate the…

If you’re running molecular dynamics simulations or exploring binding/unbinding pathways, you’ve probably encountered this question: where does the system actually go? While we often track individual atoms or align structures, it’s not always easy to get an intuitive grasp of…

One of the recurring bottlenecks for researchers running molecular simulations with GROMACS is managing input files across multiple stages: preparation, energy minimization, equilibration, and production. Errors often arise when selecting outdated or mismatched input paths, especially in multi-step workflows or…