Author: OneAngstrom

When setting up molecular simulations, especially with GROMACS, getting the selection of atom groups right is essential for accurate results and efficient analysis. This is where custom index groups come into play — a feature that can save you time…

When you’re simulating complex molecular systems, watching atoms zip across the screen can quickly become disorienting. Especially when you’re interested in closely following the behavior of a specific region—like a ligand binding site or an active catalytic domain—it’s frustrating when…

Visualizing complex molecular systems can be time-consuming, especially when you’re frequently applying recurring color schemes and representations. If you’ve ever found yourself repeatedly adjusting visualization settings in SAMSON to match your preferences, you’re not alone. Thankfully, there’s a better way…

In molecular modeling and design, visually exploring your system from different perspectives is often essential. Whether you’re preparing high-quality animations to showcase a particular biological phenomenon, or simply wish to inspect the vertical structure of a complex nanomaterial, moving the…

When creating animations in molecular modeling, one common frustration is unintended shifts in camera perspective. You carefully orient your structure, press play, and suddenly the molecule jumps or drifts—especially if you’ve been editing frames or adding content. This happens because…

If you’ve ever run long molecular simulations or relied on machine learning models for structure prediction, you know that managing computational jobs—especially remotely—isn’t just a convenience, it’s a necessity. Whether you’re using AlphaFold, NVIDIA BioNeMo models, or GROMACS simulations through…

One of the subtle but recurring challenges in molecular modeling is achieving a structure that is not only plausible but also energetically stable. Whether you’re preparing a system for a simulation, refining a molecular model from experimental data, or prototyping…