One of the most common challenges molecular modelers face when working with simulation boxes is ensuring the solute does not interact with its own periodic image. This issue, if overlooked, can lead to inaccurate simulations, affecting the reliability of results.…

Molecular modelers often struggle with understanding torsion angles—those critical rotations between parts of a molecule that influence its conformations and functions. In this blog post, we’ll explore SAMSON’s Dihedral analysis, a tool designed to simplify tracking and analyzing molecular torsions.…

Understanding how the structure of a protein evolves over time is key for molecular modelers working on protein dynamics, drug design, or molecular functions. Whether you’re studying a critical folding process or trying to identify structural stability, gaining insights into…

When preparing molecular simulations, ensuring accuracy often comes down to understanding small but crucial details. One such concept is the minimum image convention, which plays an important role in creating realistic periodic boundary conditions in GROMACS simulations. Misjudging this can…

When working on complex molecular systems, navigating and managing different selections can become a daunting task. Whether you’re analyzing ligands, receptors, or specific residues, keeping track of multiple regions of interest can slow down your workflow and distract you from…

For molecular modelers, managing complex structural models can be a challenging task, especially when working with intricate biomolecular sequences. Deep insights often require seamless mapping between a structure’s sequence, 3D Viewport, and color-coded data representations. This is where SAMSON’s Sequence…

Molecular modelers often face the challenge of optimizing protein structures effectively while ensuring all residues conform to energetically favorable regions. This process can be daunting, especially when working with complex protein models. The Interactive Ramachandran Plot tool in SAMSON provides…