Author: OneAngstrom

When building molecular animations or presentations, a common challenge is to visually track how atoms move over time. While SAMSON offers multiple ways to manipulate atomic positions — such as through simulation, docking, or manual movement — visualizing and saving…

For many molecular modelers, setting up a GROMACS simulation often starts with the same familiar workflow — downloading GROMACS, compiling it, troubleshooting library issues, and repeating the cycle on different machines or operating systems. It’s a time-consuming process that can…

Creating effective molecular animations can be time-consuming, especially when you’re trying to convey subtle structural changes or transformations in a clear and controlled manner. Whether you’re preparing a scientific presentation or building an educational visualization, you’ve probably found yourself wrestling…

Creating clear and expressive molecular visualizations can be a time-consuming task. Whether you’re working on a presentation, preparing figures for publications, or simply exploring a structure, it often involves repetitive steps: selecting atoms, applying representations, choosing color schemes, adjusting views,…

When setting up molecular dynamics simulations of membrane proteins, one of the most repetitive and error-prone steps is placing a lipid layer or bilayer around the protein. Aligning the protein, choosing the right lipid orientation, adjusting the box dimensions, and…

Creating immersive animations in molecular modeling isn’t just about rotating a protein or zooming into an organometallic complex. The real challenge often lies in guiding the viewer’s eye smoothly, helping them focus on what matters, and making the experience feel…

When creating animations of molecular processes, clarity and timing can make all the difference. Whether you’re showing molecular assembly, drug docking, or simply highlighting part of a structure, there’s often a need to make specific groups of atoms appear progressively…

Anyone running molecular dynamics simulations with GROMACS has likely come across the challenge of managing and reusing .mdp files. These parameter files are essential, but editing them manually can be error-prone. More often than not, researchers keep a cluttered folder…