When trying to communicate molecular structures and processes effectively, nothing conveys spatial relationships and dynamics better than motion. Yet, many molecular modelers still present their work using static snapshots, missing the opportunity to make insights more intuitive and memorable. Fortunately,…

When creating molecular animations in SAMSON, one common challenge that modelers face is keeping the camera viewpoint consistent throughout specific segments of the animation. This is particularly frustrating when you’re trying to highlight subtle conformational changes or focus attention on…

If you’ve ever optimized molecular geometries using traditional methods like steepest descent, you’ve probably found yourself frustrated by slow convergence—especially when working with complex systems involving large-scale atomic motions. The Fast Inertial Relaxation Engine (FIRE) minimizer in SAMSON offers a…

When preparing a protein structure for simulation, one frequently encounters the question: should I delete all the water molecules from the structure? Many molecular modelers default to removing all crystal water molecules at the preprocessing stage, but in some cases,…

Many researchers and molecular modelers benefit from integrating custom Python scripts into their molecular workflows. Whether you’re adding machine learning models, working with bioinformatics libraries, or just need a statistical package, the ability to easily install and manage Python packages…

Calculating the Potential of Mean Force (PMF) is a critical step for molecular modelers studying free energy landscapes, especially in processes like ligand binding or conformational changes. However, setting up and running a WHAM-based PMF analysis can sometimes be frustrating:…

When setting up molecular simulations, choosing the right type of unit cell can significantly impact both the accuracy and performance of your calculations. Yet, many researchers default to cubic boxes out of convenience or familiarity—often without realizing the computational advantages…

When visualizing dynamic molecular systems, it’s easy to lose track of critical components as they move during a simulation. This is especially frustrating when preparing explanatory videos or presentations: the atoms you’re trying to highlight drift off-screen, requiring constant manual…