Author: OneAngstrom

When presenting molecular systems and simulations, timing is everything. Whether you’re building educational content, preparing a presentation for a research group, or creating a guided molecular animation, there’s always one recurring challenge: how to draw attention to a specific part…

Protein docking is a powerful tool in structural biology, but one frustrating aspect many molecular modelers share is this: you set up your system, launch a docking calculation, and… the results are off. 🧬 They aren’t necessarily bad, but the…

Molecular modelers often need to inspect and modify properties of atoms or groups of atoms when preparing systems or analyzing simulations. However, editing atomic attributes can be risky: one wrong click and your structure may no longer make sense. Fortunately,…

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,…