Author: OneAngstrom

Obtaining a reliable set of initial conformations is a common challenge when setting up umbrella sampling for free energy profile calculations. Whether you’re working with protein-ligand systems or studying molecular interactions along a reaction coordinate, getting this step right is…

When preparing molecular simulations, getting the right topology can be a time-consuming task. While automatic perception of bond orders and atom types is helpful, most modelers eventually hit a point where they’d like more control: maybe the automatic perception misses…

Constructing nanotubes manually can be a tedious and error-prone process for molecular modelers. Aligning rings, duplicating atoms, merging structures, and optimizing geometry often requires significant time and care—especially if relying on custom scripts. In this post, we’ll show an alternative…

One of the most common pain points for molecular modelers is the constant need to juggle multiple tools, plugins, and scripts across different platforms just to get one workflow done. What if all of those tools could be brought directly…

When working on complex molecular systems, it’s common to switch between multiple regions of interest. You might be analyzing a ligand binding pocket, adjusting side chains of a receptor, or inspecting solvent placement. Repeatedly reselecting these components adds friction to…

Molecular modelers often face a common challenge: how to integrate functionality from external tools or scripts into their modeling platform without starting from scratch. Reproducing established workflows or re-implementing code in a new environment can be time-consuming and error-prone. If…

If you’ve ever struggled with the visual complexity of large molecular systems, you’re not alone. Molecular models are packed with detail, and sometimes it’s hard to quickly tell which atoms are buried inside a structure and which are on the…

For molecular biophysicists and structural biologists, preparing lipid bilayers around membrane proteins can be an essential yet tedious task. Whether you’re setting up simulations of transmembrane channels, studying membrane-protein interactions, or exploring lipid dynamics, aligning lipids precisely around your protein…