Running production molecular dynamics (MD) simulations can be an intimidating step for molecular modelers, particularly when it comes to ensuring that all input structures and files are correctly prepared. If you’ve ever been at a standstill because of incomplete input…

One of the recurring challenges in molecular modeling is the tedious process of creating structured molecular environments, such as solvent boxes, lipid layers, or other molecular assemblies. These are essential for preparing realistic simulation systems, but generating them from scratch…

Molecular modelers face numerous challenges when visualizing complex molecular systems. Whether showcasing a protein-ligand interaction, preparing a presentation, or simply analyzing key structural elements, much time can be wasted manually applying individual visualization settings. This post offers a solution: visual…

If you’ve ever struggled with defining the correct sampling region for ligand unbinding pathways, you are not alone. A properly defined sampling box is critical for ensuring accurate and meaningful results in studies involving molecular dynamics and ligand path finding.…

For molecular modelers, mapping ligand-pathway simulations can often be a challenge, especially when defining the ligand and its interactions precisely within a system. The Ligand Path Finder in SAMSON offers a simple way to compute ligand unbinding pathways from a…

Preparing proteins for docking, simulations, or other molecular design workflows can be time-consuming, especially when handling multiple structure files. SAMSON solves this challenge with its Batch Protein Prepare extension, making multi-file processing simple and efficient. Let’s explore how this tool…

One common challenge molecular modelers face is achieving a clear and precise visualization when undocking molecules or parts of a structure. SAMSON, the integrative molecular design platform, provides a great solution with its Undock animation. However, many users might not…

Every molecular modeler has experienced this: You’re deep into designing a complex molecular system, carefully adjusting structures, and then… suddenly, a single unintended action derails your progress. Fear not—SAMSON’s History view has you covered! Let’s explore how leveraging the undo…