Author: OneAngstrom

For computational molecular modelers, efficient scripting and workflow automation can feel cumbersome without a robust system to manage dependencies and libraries. Integrating specific Python packages into your modeling pipeline can open up incredible possibilities—from deep learning algorithms to advanced statistical…

Umbrella sampling is a powerful technique in molecular modeling, enabling researchers to understand the energetics along a reaction coordinate. But implementing it can feel daunting, especially when you’re faced with setting up reaction-coordinate windows and managing simulations efficiently. With the…

For molecular modelers, keeping attention focused on specific parts of a molecular system during animations can be challenging, especially when analyzing dynamic processes without letting your perspective drift. The "Look at atoms" animation in SAMSON offers an elegant solution by…

Preparing protein structures for molecular modeling tasks such as docking, simulations, or binding-energy calculations can be a tedious and error-prone step. Ensuring your model is clean and valid is essential to avoid unnecessary issues later in the workflow. SAMSON offers…

Molecular modeling often involves extracting meaningful insights from simulation data, and one common challenge researchers face is processing umbrella sampling data to compute the Potential of Mean Force (PMF). If your workflows involve GROMACS simulations and you find compiling PMF…

For molecular modelers, a significant challenge can be presenting complex molecular structures and systems with clarity. Often, the ability to smoothly shift camera views plays a critical role in ensuring that a molecular animation truly communicates the right details to…

As molecular modelers, presenting your models effectively is integral to your work. Whether you’re showcasing your latest breakthroughs or dissecting microscopic systems for insights, visual clarity matters. One tool within the SAMSON platform to enhance these presentations is the Flash…