Author: OneAngstrom

Adapting molecular dynamics simulations to specific systems often requires precise control over simulation parameters. However, editing .mdp files manually or ensuring consistency across simulation steps—like energy minimization, NVT/NPT equilibrations, and production runs—can be time-consuming and error-prone. If you’re working with…

If you’ve ever tried to isolate a specific subset of atoms in a complex molecular structure for visualization, simulation, or manipulation, you know how time-consuming and frustrating it can be. Manual selection becomes inefficient very quickly. Whether you’re targeting a…

When analyzing molecular simulations, it’s often crucial to focus on a specific part of your system — a binding site, an interface, or a reactive center — as atoms move through time. But there’s a common frustration: if you want…

Running molecular dynamics (MD) simulations can be time-consuming and compute-intensive — especially on large biomolecular systems. Molecular modelers frequently face the challenge of limited local computational resources. And while high-performance computing facilities are an option, they often involve complex setup…

Analyzing molecular simulations often means reviewing complex motions over many frames of a trajectory. For modelers studying folding patterns, automated docking, or multistep reactions, reviewing these paths backward can reveal behavior that is missed in typical forward playback. If you’ve…

When setting up molecular dynamics simulations, embedding a protein within a lipid membrane can be time-consuming and error-prone. Whether you’re studying membrane proteins, simulating transmembrane transport, or modeling realistic biological environments, creating these lipid environments from scratch often requires multiple…

If you’re working in materials science, computational chemistry, or crystallography, you’ve probably run into the challenge of understanding how atomic defects influence crystal properties. Whether you’re studying mechanical strength, thermal conductivity, or electronic behavior, point defects—like vacancies or substitutional impurities—can…