During a molecular modeling session, many scientists and educators aim to produce smooth, visually clear animations that reflect the dynamic behavior of molecular systems. Whether it’s for simulations, educational videos, or collaboration, capturing the motion of atoms as they transition…

Modeling molecular systems isn’t just about setting up simulations—it’s also about experimenting, tweaking, and interacting with models in real time. But what if you’re unsure how your molecular system will respond when atoms are moved manually during a simulation? If…

If you’ve ever found yourself wasting time manually repositioning your molecular view again and again while switching between different regions of interest, you’re not alone. Navigating complex molecular structures is part of every modeler’s workflow—but constantly rotating, zooming, and centering…

Installing scientific software can often be a roadblock for molecular modelers, especially when strict system permissions or IT policies come into play. If you’ve ever faced the frustrating message that admin rights are required just to install a visualization or…

One of the common challenges faced by molecular modelers when performing Potential of Mean Force (PMF) calculations is preparing the input folder structure for the Weighted Histogram Analysis Method (WHAM). If you’ve tried setting everything up manually, you might have…

For many molecular modelers using GROMACS, editing .mdp (molecular dynamics parameter) files manually has long been the norm. It’s effective but error-prone, especially when experimenting with different simulation setups like energy minimization, equilibration (NVT, NPT), or production runs. Copy-pasting parameters,…

When working with molecular structures derived from NMR data, it’s common to run into geometry issues — atoms slightly out of place, bond lengths that don’t look quite right, and overall structural elements that need relaxation. Cleaning up these initial…

If you’ve ever tried to present complex molecular systems and felt limited by flat, static perspectives, you’re not alone. One common challenge in visualizing molecular models is finding ways to create depth and a natural sense of movement—especially in a…

When designing molecular presentations, clarity often hinges on what you choose to show—and just as importantly, what you choose to hide. The Conceal atoms animation in SAMSON offers a simple way to make atoms—and the bonds between them—disappear progressively. This…