Author: OneAngstrom

For molecular modelers working with proteins, understanding symmetry is often a key step in designing molecular structures or simulating interactions. Crystallographic units and biological assemblies provide critical insights into protein organization, but deriving symmetry mates from these data can sometimes…

Molecular modeling often involves complex calculations and parameter setups, and for many researchers, streamlining these processes is key to productivity. The Universal Force Field (UFF) in SAMSON offers a robust tool for simulating molecular systems, but figuring out how to…

Have you ever struggled with deciding the best way to set up your periodic boundary conditions (PBC) in molecular simulations? The choice of unit cell can significantly impact performance and accuracy, especially when you’re simulating systems like macromolecules in solution.…

One of the most significant challenges for molecular modelers is the need to rapidly and precisely edit molecular structures during the design process. SAMSON, the integrative molecular design platform, addresses this challenge through its versatile editors, which enable a wide…

For molecular modelers aiming to present visually compelling and scientifically accurate representations, mastering material customization is a critical step. Materials enrich your molecular visualizations, making them resonate with both realism and clarity. With SAMSON’s integration of the Cycles Renderer, you…

Umbrella sampling is a powerful method for exploring potential of mean force (PMF) landscapes, but setting it up often feels like a complex puzzle for molecular modelers. If you’ve been looking for a way to simplify and automate this critical…

Molecular modelers often face the challenge of scaling up their workflows—whether it’s simulating multiple conformations of a molecular system or analyzing different systems with consistent parameters. Efficiently running such batch computations is crucial to save time and ensure reproducibility. The…

For molecular modelers, one common challenge is presenting molecular dynamics without losing critical structural details. Imagine needing to communicate your findings where the essential part of a complex system remains stable while other parts follow their motion. Enter the ‘Hold…

Molecular modeling often involves visually analyzing the behavior of particle groups or molecules in various scenarios. One tool to achieve this in an intuitive and interactive way is the Rotate animation feature in SAMSON. This post will guide you on…