Molecular animations are more than just eye candy—they’re essential for communicating structural transitions, mechanisms, and design ideas. But what happens when certain parts of a model clutter your scene or distract from the key mechanism you’re trying to convey? Whether…

Communicating molecular mechanisms clearly can be a challenge. Whether you’re creating visuals for publications, lectures, or lab meetings, the way you represent the spatial context of your molecules—and how that context changes over time—really matters. This is where camera animations…

When analyzing molecular simulations or trajectories, a common challenge for molecular modelers is keeping focus on a specific group of atoms as they move over time. Whether you’re preparing a presentation, exploring a dynamic mechanism, or sharing a molecular movie…

One of the most common frustrations among molecular modelers using GROMACS is the seemingly simple—but often error-prone—task of selecting the correct input structure when launching production Molecular Dynamics (MD) simulations. It might happen that after spending hours on system setup…

Getting started with integrative molecular modeling often feels like learning a new language. Which buttons to click? How to visualize data? What’s the right workflow for building or analyzing a molecular system? These are common questions, especially for researchers, students…

When you’re creating molecular animations, getting the right camera movement can be challenging. You may want to create visualizations that rotate elegantly around specific molecular structures or frame the subject from just the right angle. But doing this frame-by-frame can…

When automating molecular modeling tasks in SAMSON, many users run into a common issue: how to replicate interactive operations in Python scripts. Whether you’re adding hydrogens, changing color schemes, or setting a visual preset, doing it once through the interface…

For many molecular modelers, the first step in gaining insight from a structure is being able to see it clearly. But visualizing complex biomolecular systems can be time-consuming. Choosing how to represent atoms, bonds, chains, ligands, and setting rendering parameters…

When working with coarse-grained (CG) molecular simulations, many modelers run into unexpected behavior during solvation—particularly with Martini models. This blog post dives into why solvent setup in the GROMACS Wizard in SAMSON requires an extra step, and how skipping it…