Author: OneAngstrom

One of the most frequent issues faced when interpolating between protein conformations is something many don’t anticipate: disconnected molecular structures. If you’ve ever encountered the error message “Cannot proceed because the structure does not make one connected component” while using…

Precise control over molecular geometries is a core part of any modeling or simulation workflow. Whether you’re adjusting a ligand orientation, fine-tuning a molecular assembly, or preparing a structure for simulation, moving atoms and molecular fragments accurately is essential. This…

Understanding how molecules interact at the atomic level can make or break a drug discovery or molecular design project. Yet, identifying and interpreting specific interactions—hydrogen bonds, steric clashes, aromatic stacking—can be tricky, especially when working solely in 3D. This is…

In molecular modeling, visual clarity is essential when communicating complex structures and mechanisms. Whether you’re showcasing a protein-ligand interaction or preparing an educational molecular scene, the way elements appear and disappear can greatly influence how well your audience understands molecular…

Running molecular dynamics simulations often requires significant computational resources — the kind most laptops or even desktops can’t provide for large or long simulations. For many molecular modelers, this turns an exciting project into a frustrating wait. One elegant solution…

For researchers modeling molecular systems involving carbon nanotubes (CNTs), quickly generating realistic nanotube structures is both essential and sometimes surprisingly tedious. Whether you’re running mechanical simulations, building nanochannels, or prototyping NEMS, manually defining chirality vectors or adjusting radii via parameter…

Choosing the right force field is a recurring concern for molecular modelers, especially when dealing with non-standard molecules or specific biochemical conditions. While GROMACS provides several standard force fields, sometimes they just don’t cut it—especially when you need to simulate…

If you’ve ever opened a PDB file and been disappointed to find only part of the structure—just one chain or a fragment of a protein complex—you’re not alone. Many researchers assume PDB files always include the full biological assembly. Instead,…