Author: OneAngstrom

Interactive molecular minimization is critical in model refinement, but what if you need to relax only a specific region of a large molecule, without moving the rest? This need frequently arises in structure preparation — whether after adding atoms, modifying…

One common challenge in molecular modeling — especially in nanotechnology, materials science, or biophysics — is replicating complex structural motifs across different geometrical arrangements. Whether you’re trying to build a carbon nanotube, create a crystalline structure, or arrange proteins in…

Reproducibility is a core concern in molecular modeling. Whether you’re publishing results, working with legacy systems, or using specific patches, there are situations where the default GROMACS installation — even the latest one — just won’t do. Fortunately, the GROMACS…

When presenting complex molecular simulations, one of the common challenges is pacing. Animations often move too quickly, not giving viewers enough time to fully observe important transitions, interactions, or structural changes. Whether you’re sharing a ligand binding pathway or a…

Visualizing molecular motion can be essential when preparing presentations or explaining a structural change to collaborators or students. However, animating groups of atoms in a way that is both informative and visually smooth can be time-consuming, especially if each movement…

One of the most common challenges in molecular modeling is sharing complex research setups with peers, collaborators, or even your future self. Whether it’s a protein-ligand setup, a molecular simulation system, or a visual analysis, reproducing someone else’s work—or rediscovering…

Creating effective molecular animations often involves more than just showing or hiding entire structures. A common challenge among molecular modelers is presenting complex mechanisms or transitions without overwhelming the viewer. One useful way to guide attention is to progressively conceal…