Author: OneAngstrom

Equilibration in molecular dynamics is an essential step before launching production simulations. But even experienced molecular modelers sometimes hit snags during the NVT (constant particle number, volume, and temperature) equilibration phase. This blog post explores how to avoid common setup…

When working on molecular design projects, sharing results and configurations across a team can be both essential and challenging. Whether you’re collaborating with researchers in your lab, students, or external contributors, it’s important to provide access to the right documents…

Creating carbon nanotubes is a common task in nanoscale design. Despite being conceptually simple, the manual construction of these tube-like structures with regular periodicity, seamless curvature, and proper bonding alignment can be time-consuming and technically tricky — particularly when high…

Running simulations on a single molecular structure is common practice, but what if you have many starting conformations of the same molecule? Whether you’re studying flexibility, rare events, or preparing umbrella sampling, working with many initial conformations can quickly become…

One of the most frequent pain points in molecular modeling is restarting a simulation step after modification or failure. If you’ve ever run a protocol, reached the equilibration stage, and then had to dig back through directories to track down…

One of the recurring challenges in molecular modeling is how to effectively convey localized, subtle motions in complex molecular systems. Whether you’re preparing a presentation or a visual abstract for a paper, clearly illustrating conformational dynamics in a way that…

When you’re visualizing molecular dynamics, it’s common to focus on a specific region of your system—maybe a crucial ligand, or a flexible protein loop. But as the simulation unfolds, that region often drifts out of view. You’re left constantly adjusting…

One challenge many molecular modelers face is bridging the gap between specialized external tools and their main modeling platform. Whether it’s docking software, simulation packages, or web-based services, integrating these into a single workflow often means jumping through file conversions,…

Creating animations of molecular structures can be a powerful way to communicate scientific results. But often, modelers struggle to frame their molecules in a visually smooth and structured way. An all-too-common issue: static or jerky camera movements that fail to…

If you’re working with molecular docking, structural analysis, or simulations across many proteins, you’ve likely run into this challenge: preparing dozens or even hundreds of raw PDB files manually. Stripping water, removing unnecessary ligands, adding hydrogens, resolving alternate locations… doing…