Author: OneAngstrom

When creating molecular animations, it often becomes necessary to shift focus, reduce visual noise, or reveal features step-by-step. Instead of abruptly switching views or hiding atoms instantly, a more refined approach is to progressively hide atoms and bonds over time.…

One of the most practical challenges in molecular modeling is verifying whether your molecular system behaves as expected during deformation — for example, when an atom is displaced from equilibrium. Traditional simulation setups often involve long preparation workflows and delayed…

Have you ever run a simulation where the pressure never quite stabilizes? Or where your system density keeps drifting, despite starting from an apparently well-prepared structure? If so, you’re not alone. One of the trickiest aspects of preparing a molecular…

When using ARAP (As-Rigid-As-Possible) Interpolation to generate protein conformational transitions, an essential but sometimes overlooked step is how the structural connectivity—also known as ARAP edges—is defined. For molecular modelers preparing simulations or building transition pathways, getting the connectivity right can…

Free energy calculations of ligand binding or unbinding can be extremely powerful—but preparing input files often feels more painful than productive. One recurring challenge is extracting the atomic coordinates of molecules along a computed reaction path. If you’ve ever run…

Creating molecular animations isn’t just about visualizing structures—it’s about communicating insights clearly. When zooming into molecular systems, many researchers use the Zoom camera effect in SAMSON. But there’s a subtle limitation: it only moves the camera along its view direction,…

Molecular modelers often face a recurring challenge when studying conformational changes in large biomolecular systems: how to generate a realistic trajectory between two known structural states. This issue becomes more complicated when the two states differ significantly, as is the…

Setting up GROMACS for molecular dynamics simulations can be a real roadblock for many researchers. Between compiling the package, ensuring all dependencies are correctly met, and navigating version compatibility issues, it’s no surprise that time is often spent troubleshooting before…