Author: OneAngstrom

If you’ve ever run a molecular dynamics simulation only to see your system blow up 🔥 right after energy minimization, you’re not alone. One of the most frequent issues molecular modelers face is rushing into full simulations without proper temperature…

When working with complex molecular systems, it’s often not enough to merely show a static view⎯you need to communicate how one part of a molecule relates to another, highlight conformational changes, or just produce more engaging visualizations. This becomes especially…

Tracking how ligands unbind from biomolecules is critical for understanding molecular interactions — but visualizing this process across a simulation trajectory can be tricky. A common struggle among molecular modelers is identifying and presenting meaningful movement without overwhelming the viewer…

When modeling at the nanoscale, researchers, educators, and engineers often need to quickly generate accurate carbon nanotube (CNT) structures. Whether you’re simulating molecular transport, designing nanoelectromechanical systems, or visualizing nanoscale materials, building CNTs manually can become repetitive and error-prone. The…

Molecular animations can quickly become overwhelming when dealing with complex structures, especially when multiple elements appear and disappear during a presentation or simulation. A frequent challenge for molecular modelers is ensuring clarity in dynamic visualizations: how do you focus attention…

Many molecular modelers rely on the GROMACS engine for performing complex molecular dynamics simulations. While using the default versions bundled with visualization platforms is convenient, there are valid reasons to switch to a custom GROMACS version for local jobs. Whether…

When studying the dynamics of complex molecular systems, one of the challenges modelers often face is visual clarity: how to keep visual focus on specific atoms or molecular fragments as they move throughout a simulation. If you’ve ever found yourself…

Setting up lipid membranes around proteins can be a time-consuming and error-prone task in molecular modeling workflows. If you’ve ever tried to manually create lipid bilayers and fit them around membrane proteins, you know how tricky it can get—from orientation…