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…

Understanding how a ligand exits a protein’s binding pocket is critical in molecular modeling and drug discovery. Researchers often simulate multiple unbinding pathways, but visualizing and comparing them in a clear and interpretable way can be challenging. A clean visual…

One common frustration in molecular simulations is starting a production run only to realize later that the system wasn’t properly equilibrated. This often leads to inaccurate results, wasted computing time, or simulations that eventually crash. A frequent culprit? Skipping or…

Tracking specific atoms during a molecular simulation is essential when studying dynamic systems, such as interactions in flexible biomolecules or complex molecular assemblies. But how can you keep the camera focused on the part of the system that matters—without manually…

Molecular modelers working with GROMACS know the importance—and the complexity—of setting the right molecular dynamics parameters. Whether it’s energy minimization, NVT/NPT equilibration, or production simulations, configuring .mdp (molecular dynamics parameter) files can become a time-consuming part of the workflow, especially…