Author: OneAngstrom

Preparing membrane-protein systems for simulation is a task that molecular modelers regularly face, especially when modeling transmembrane proteins. However, manually inserting lipids and ensuring proper alignment around a protein can be time-consuming and error-prone. If you’ve ever tried to construct…

Molecular modeling often requires precise visualization to communicate structural insights clearly — whether in academic papers, presentations, or team meetings. But framing your molecular system from the right angles can be time-consuming, especially if you’re repeatedly adjusting views to get…

Running umbrella sampling simulations is only part of the story in calculating a Potential of Mean Force (PMF). A common challenge molecular modelers face is realizing—too late—that parts of the reaction coordinate space were not well covered, leading to unreliable…

One of the most common frustrations in molecular modeling is constantly reconstructing the same types of visualizations: highlighting ligands, showing ribbons for proteins, zooming in on active sites, choosing color schemes, and setting up camera perspectives. When models become complex,…

When preparing animations for scientific presentations or teaching materials, molecular modelers often face a common challenge: how to clearly show the removal or disappearance of molecular parts without making the transition feel abrupt. Using simple hide/show toggles can break the…

For molecular modelers preparing systems for molecular dynamics simulations, a key challenge is achieving accurate thermodynamic conditions before production runs. One critical step in this process is NVT equilibration, which brings the system to the desired temperature while maintaining constant…

Many molecular modelers and computational chemists have their own Python packages—for custom simulations, analysis pipelines, or even neural networks for property prediction. But using them often means jumping between development environments, terminal sessions, and structured molecule viewers. What if everything…

One common challenge in molecular dynamics is ensuring that your system reaches and maintains the desired temperature before you proceed with production simulations. If the temperature isn’t properly stabilized, results can be unreliable or misleading. This is where NVT equilibration…