Author: OneAngstrom

Running molecular dynamics (MD) simulations can take a significant toll on local hardware, especially when simulating large systems or running long trajectories. Many researchers face the challenge of not having access to high-performance computing infrastructure when they need it most.…

When working with complex molecular structures, showing the right detail from the right angle can change everything. Whether you’re preparing content for a presentation, teaching a concept, or demonstrating a simulation result, camera motion matters. A lot. One common obstacle…

One of the most frustrating issues for molecular modelers using GROMACS is running an NPT equilibration—only to find that the system’s density is still oscillating or far from expected. If you’re spending time wondering whether you need to restart, modify…

Accessing the right computational tools at the right moment can make a big difference in molecular modeling workflows. Whether you’re preparing a docking simulation, visualizing biomolecular systems, or connecting to external services, having quick access to the right functionality can…

One common frustration in molecular modeling is the disconnect between model manipulation and immediate feedback. Molecular designers frequently spend time adjusting structures and running batch simulations, only to repeatedly refine parameters through a slow trial-and-error cycle. What if changes could…

When dealing with complex molecular systems, manually selecting atoms, residues, or ligands can quickly become tedious—even frustrating. If you’ve ever found yourself zooming and clicking around just to isolate one component of a protein-ligand complex, this post is for you.…

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…