Author: OneAngstrom

When setting up molecular dynamics simulations, especially using GROMACS, researchers often face a surprisingly impactful decision: what shape should the simulation box be? Choosing the right periodic unit cell shape can significantly reduce computational costs and resource usage, especially when…

In molecular modeling, aligning full protein structures is a common task—especially when comparing proteins from different organisms or assessing mutations. But what happens when you’re only interested in a specific functional domain or a particular secondary structure? This is a…

In collaborative molecular modeling projects, especially in academic and interdisciplinary environments, it is often difficult to keep track of who is doing what. Profiles end up being scattered across platforms, documents shared by email or chat, and institutional pages remain…

For many molecular modelers, gaining fine control over simulations goes beyond simply setting up a system. Often, it’s just as important to define custom groups of atoms or residues for analysis, restraints, or biasing methods like umbrella sampling. This is…

When presenting molecular models, it’s often crucial to bring attention to specific components at the right time. Whether you’re preparing a video for a conference talk, a class, or your research group, you’ve probably faced the challenge of controlling what’s…

One common challenge in molecular modeling is illustrating conformational transitions—especially when you only have two experimental structures available. Whether for presentations, publications, or hypothesis generation, animating molecular transitions can help reveal critical insights quickly. But interpolating between two states manually…

When working with protein structures in molecular modeling, small inconsistencies can turn into major computation roadblocks. If you’re setting up a conformational transition, umbrella sampling, or just trying to interpolate between two protein forms, issues like alternate atom locations, water…

Color is more than aesthetics when it comes to molecular modeling—it’s a functional layer that reveals structural patterns, properties, and meanings at a glance. Whether you’re analyzing temperature factors, chain identities, or hydrophobic regions, having the right color scheme helps…

In molecular modeling, comparing protein structures is a frequent and essential task—whether you’re identifying conserved structural motifs, evaluating mutant effects, or building homology models. But what happens when you’re only interested in a specific structural feature, like an active site…