As molecular systems grow in size and complexity, adding labels to specific atoms, residues, or molecules can be a great way to identify and present the most relevant parts of your structure. However, it’s easy for labels to become overwhelming,…

Preparing ligands for docking can feel like a minor step, especially when your molecular modeling workflow is already complex. But overlooking ligand minimization can lead to misleading docking results and longer computation times. In this blog post, we’ll walk through…

For researchers in molecular simulation, computing Potential of Mean Force (PMF) profiles can be an involved task—especially when dealing with data from multiple umbrella sampling simulations. Manual WHAM (Weighted Histogram Analysis Method) workflows in GROMACS often require scripting, data formatting,…

When you’re building molecular models, clarity is everything. Whether you’re preparing a presentation, creating an educational resource, or documenting complex systems, annotations and visual cues can make your work much more effective. One underused but essential feature in SAMSON is…

Analyzing protein–ligand interactions is a key step in molecular modeling and drug design. Whether you’re a student, researcher, or experienced computational chemist, you’ve probably found yourself trying to figure out a fast and visual way to confirm whether your ligand…

In molecular modeling, attention to detail is everything. Whether you’re preparing a presentation, illustrating a mechanism, or crafting an educational video, highlighting specific structures—while letting others momentarily disappear—can improve clarity and focus. However, manually fading parts of a structure in…

Preparing a molecular system for simulation often involves tedious geometry optimization. Many modelers still use steepest descent by default, even though it’s not always the most time-efficient approach, especially with larger systems or flexible molecules. If you’ve ever waited too…

Running molecular dynamics (MD) simulations may sound routine, but if you’ve ever seen unstable temperatures, crashing systems, or hours of lost compute time, you know how crucial getting equilibration right is. One often overlooked challenge is setting up the NVT…

For many molecular modelers, managing simulation workflows can become complex when switching between tools, environments, and machines. If you’re using GROMACS for molecular dynamics, you probably know the challenges involved with setting up simulations locally: installation and compilation, environment configuration,…