Author: OneAngstrom

If you’ve ever run umbrella sampling simulations and found yourself stuck at the next step—extracting the Potential of Mean Force (PMF)—you’re not alone. PMF profiles help interpret free energy landscapes, crucial in understanding molecular interactions, binding affinities, and conformational changes.…

One frequent challenge molecular modelers face when creating animations is how to naturally zoom into a region without locking the camera onto a single, rigid point of focus. Whether highlighting a binding site, exploring internal cavities, or guiding the viewer…

For molecular modelers and drug designers, covalent docking is often seen as a complex and time-consuming task. It typically requires careful preparation of ligands and receptors, as well as software tools that can accurately model the formation of covalent bonds…

Animations play a crucial role in communicating complex concepts in molecular modeling. However, a common challenge arises when trying to illustrate scenarios where some atoms need to stay put while others move—such as docking, conformational changes, or assembling molecular complexes.…

When modeling complex molecular systems, geometry optimization is often the first step before moving on to property predictions, docking studies, or simulations. But what if you could optimize your molecules while interacting with them—dragging atoms and watching the structure adapt…

When working on molecular animations, it’s common to encounter a challenge: how do you isolate the motion of certain atoms or groups while keeping others perfectly still? Whether you’re preparing a presentation to highlight a binding site mechanism or illustrating…

If you’ve ever created a molecular animation and felt frustrated by the sudden appearance or disappearance of molecular structures, you’re not alone. Many molecular modelers want to smoothly introduce structures over time, especially when visualizing things like conformational changes, ligand…

When creating molecular animations or presentations, clarity and continuity matter. It’s easy to overlook how changes in the camera view can disrupt the flow of a molecular video or compromise the viewer’s understanding. Have you ever looked back at an…

The frustration is familiar to many molecular modelers: you’ve built or downloaded a molecular structure, set everything up for a simulation, only to find out that your model contains steric clashes or non-ideal geometries that cause your simulation to crash…