Author: OneAngstrom

Working with systems that involve multiple copies of the same protein is increasingly common in coarse-grained molecular dynamics simulations — especially when simulating crowded environments or modeling self-assembly. Tools like Martinize2 help generate coarse-grained (CG) topologies for the MARTINI force…

Creating accurate molecular models of carbon nanotubes (CNTs) can be time-consuming—especially when you want a specific chirality, direction, or length. Manually inputting parameters is precise, but sometimes inspiration is better expressed visually. If you’ve ever found yourself wishing you could…

In molecular simulations, tracking the motion of binding partners, domains, or other parts of a system can quickly become overwhelming. Many molecular modelers manually inspect coordinate files or visualize entire trajectories, making it difficult to focus on the actual motion…

In molecular modeling, visual clarity matters—especially when you’re dealing with complexes where molecules interact closely, such as in docking studies or protein-ligand interactions. If you ever presented your model and found yourself thinking, “I wish I could just show how…

When working in molecular modeling, clear visual communication is just as important as robust computational results. For example, when you’re preparing a presentation or video to explain the structure or function of a molecule, it’s important to guide the viewer’s…

In molecular modeling, identifying realistic transition paths between conformational states is often essential—whether you’re exploring ligand unbinding, folding pathways, or chemical reaction mechanisms. Yet, even with tools that generate trajectories, like linear interpolation or sampling-based methods, the paths can be…

When crafting molecular animations—whether for a research talk, a publication, or a classroom—visual clarity plays a major role. Still, one detail that’s easy to overlook is the transition between visual scenes, especially when presenting sequences with completely different molecular representations,…

Running molecular dynamics (MD) simulations with GROMACS can be resource-intensive, particularly when working with large systems or long time scales. If you’ve ever been limited by computational power on your local machine — or had to abandon simulations partway through…