Author: OneAngstrom

If you’ve ever tried to model carbon nanotubes (CNTs), you’ve probably run into the challenge of selecting the right n and m parameters. These parameters define the chirality and radius of a CNT—fundamental structural elements that impact its electronic and…

Molecular modelers working with large biological systems like viral spike proteins often face the challenge of understanding conformational motions — especially when experimental data is limited to static states. This becomes particularly important for studying viral entry mechanisms, such as…

Collaboration is a central part of the molecular modeling workflow. Whether working across research teams, departments, or institutions, scientists often need to exchange complex molecular data. However, molecular structure files can come with numerous dependencies, metadata, and large associated datasets.…

Visualizing molecular trajectories is essential for understanding complex behaviors such as conformational changes, docking events, or transitions between molecular states. But synchronizing multiple paths or smoothly animating a recorded trajectory can be challenging—especially when the number of frames doesn’t match…

Integrating complex tools is often a roadblock for molecular modelers. Whether it’s accessing external software, running simulations, or visualizing structure-function relationships, the ecosystem can feel fragmented. You’re forced to juggle between environments — installing plugins, converting file formats, or writing…

Before running molecular simulations or refining homology models, it’s important to ensure your structure is sound. One common problem? Backbone conformations that fall into disallowed regions of a Ramachandran plot. These typically indicate strained residues, which can affect the stability…

When working on multi-layered molecular design projects, clarity and structure are essential. Whether you’re modeling a protein-ligand interaction or managing multiple systems in parallel, organizing your data hierarchy efficiently can save hours of repetitive work—and more importantly, reduce error. That’s…

Molecular modeling is as much about creativity and exploration as it is about precision and technique. But if you’ve ever found yourself caught in a repetitive series of adjustments — selecting atoms, transforming structures, or generating new components — then…

Preparing for a ligand unbinding simulation in molecular modeling isn’t just about running an algorithm—it’s about setting up your system correctly so that the underlying method can do its job properly. One of the most important steps, often underestimated, is…

Anyone working with molecular dynamics knows that skipping proper charge neutralization of your system can cause serious artifacts during simulation. From incorrect electrostatics to instabilities during energy minimization, imbalanced systems can quietly sabotage your simulation before it even begins. Thankfully,…