Author: OneAngstrom

When working with complex molecular systems, especially when comparing molecular structures, preparing input for simulations, or visualizing assemblies, it’s important to have your structures neatly positioned and consistently oriented. Yet too often, molecular modelers find themselves manually adjusting atoms and…

If you’ve ever spent too long trying to create a smooth molecular docking animation—manually adjusting atomic positions or writing complex scripts—you’re not alone. Visualizing docking movements between molecules or between a ligand and a receptor can be time-consuming, especially when…

One common challenge in molecular simulations is determining whether you’ve sampled enough along the reaction coordinate during umbrella sampling. Incomplete coverage can lead to artifacts in the computed free energy profiles, making them unreliable. If you’ve ever spent days running…

Have you ever zoomed into your molecular system in SAMSON and wondered where your carefully added labels went? Or perhaps you stepped back from a large complex and the labels cluttered the view? If you work with molecular models and…

When setting up molecular dynamics simulations, especially in biological or materials science contexts, one often faces an overwhelming number of choices. One such choice that significantly impacts both simulation accuracy and performance is the shape of your unit cell used…

When simulating molecular mechanisms, such as how a ligand unbinds from a protein, researchers often face a specific challenge: known initial and final states of a system are available, but the energetically plausible path that connects them is not. This…

Creating accurate carbon nanotube (CNT) models is a common yet often cumbersome task in molecular design and nanoscience. Whether you’re preparing nanostructures for simulation or designing nanoscale devices, defining geometry and chirality vectors manually can interrupt your workflow. But what…

When working on molecular presentations, particularly those involving systems like membranes, surfaces, or long assemblies (e.g., DNA or polymer chains), it’s often essential to maintain a consistent perspective while shifting the viewpoint across the structure. A common challenge arises: how…