Author: OneAngstrom

Molecular modelers working with free energy profiles often rely on umbrella sampling simulations to explore potential energy surfaces along reaction coordinates. But once the simulations are done, a common pain point remains: how do you efficiently compute high-quality Potential of…

For many molecular researchers and modelers, writing Python scripts to automate modeling tasks can feel like a necessary chore. Whether it’s selecting atoms based on spatial constraints, building user interfaces, or computing molecular properties, scripting can be powerful—but also time-consuming…

Working on complex molecular modeling workflows often means tapping into the wealth of Python’s ecosystem—NumPy for computations, SciPy for simulations, PyTorch for deep learning, and more. But for many scientists, switching between a terminal, a code editor, and a molecular…

Understanding complex biomolecular structures often involves navigating dense 3D environments filled with atoms, ribbons, and other intricate representations. But even with the most accurate geometry, sometimes something just “feels off” — flat visuals that make it difficult to distinguish between…

When working with complex molecular models, even simple tasks like finding and editing a property of a specific atom can become overwhelming. If you’ve ever spent too much time scrolling through long lists of atomic attributes or lost track of…

For many molecular modelers, switching between apps, editors, and panels slows down their workflow. While SAMSON provides a rich and modular interface, not everyone realizes just how customizable it is. If you ever thought, “I wish this panel were over…

When working with molecular dynamics simulations in GROMACS, one common challenge is defining atomic groups for analysis, restraints, or pull codes. By default, GROMACS generates some standard index groups (like Protein, Water, or Ion) automatically. But what if you need…