Author: OneAngstrom

One of the key challenges in molecular dynamics simulations is ensuring your system reaches and maintains a stable target temperature before production runs. For many molecular modelers, this step — known as NVT equilibration — can be a source of…

For many molecular modelers, scripting can be both empowering and intimidating. Python gives you immense control over molecular systems in SAMSON, but what if you’re not confident with the syntax? Or you just want to speed things up? SAMSON AI…

Molecular modelers often rely on automatic perception tools to assign atom types and bond orders, which keeps simulations quick and intuitive. However, these automated systems may not always capture specific bonding environments or unusual structures, leading to inaccuracies in energy…

Capturing the right moment in a molecular animation can be challenging. If you’ve ever struggled with emphasizing a small region of a large biomolecular system—without changing the visual context or disturbing focus effects—then you’re not alone. One commonly overlooked solution…

One common challenge when performing protein-protein docking is the high number of docking solutions that turn out to be incorrect upon detailed inspection. Especially when the potential binding site is already known, a full-sphere unconstrained search wastes time and resources,…

Modeling molecular systems often involves calculating the Potential of Mean Force (PMF) along a reaction coordinate. This can be essential for understanding binding affinities, reaction mechanisms, and free energy landscapes. However, performing a PMF analysis—especially assembling and processing multiple simulation…

When preparing molecular presentations, communicating structure and dynamics clearly can be a challenge. Static images often miss the 3D context, and manually aligning frames for a flyaround animation can be time-consuming and imprecise. Fortunately, if you’re using SAMSON, the Orbit…