Author: OneAngstrom

If you’ve ever tried to edit a whole group of atoms in your molecular model—maybe to reposition a residue without disturbing the relative geometry of its atoms—you might have found it tricky to avoid collapsing everything into a single point.…

Sharing molecular modeling workflows with colleagues or students often involves zipping together input files, scripts, images, and documentation — and hoping they preserve the folder structure when unpacking. But what if you could combine everything — models, scripts, data, and…

One of the common frustrations in protein-protein docking is the large number of false positives that arise from unconstrained searches. Molecular modelers often spend excessive time manually filtering docking results, only to realize that many of the proposed orientations are…

When working on complex molecular systems, one common problem modelers face is the need to edit properties of multiple entities—such as atoms—simultaneously. Whether you’re adjusting atomic positions, changing atom types, or reviewing structural attributes, doing it one atom at a…

When working with molecular systems in GROMACS, detailed analysis and advanced simulation setups such as umbrella sampling or pulling simulations often require specific selections of atoms or residues. These selections are managed using index groups. GROMACS automatically generates standard index…

Anyone who has worked with multiple protein structures knows the challenge: each file needs cleanup before starting a molecular dynamics simulation, docking calculation, or structural analysis. Removing water, handling alternate locations, fixing missing hydrogens—it’s the sort of repetitive task that…

In molecular dynamics simulations, the Energy Minimization (EM) step helps relieve atomic clashes and brings the system to a physically realistic starting point. It’s often one of the first steps after preparing your system, but sometimes it just won’t converge—and…

Molecular simulations often involve tracking complex atomic rearrangements: docking events, folding pathways, or drug interactions. But replaying those subtle moves isn’t always straightforward. If you’ve ever needed a clean, visual representation of how atoms moved throughout a simulation for presentations…

Molecular modelers often face a recurrent frustration when studying large biomolecular structures: the lack of dynamic, visual insight into conformational transitions. This is particularly true for complex glycoproteins like the SARS-CoV-2 spike protein, which plays a central role in viral…