Author: OneAngstrom

When working with protein-ligand systems, one of the recurring challenges in computational modeling is understanding how a ligand exits its binding site. The process isn’t always intuitive, especially in complex or embedded binding pockets. SAMSON’s Ligand Path Finder app offers…

For molecular modelers and nanoscientists working with carbon nanotubes (CNTs), setting up accurate atomic models can be a time-consuming and error-prone process. Whether you’re studying transport mechanisms, conducting materials simulations, or designing nanodevices, being able to generate and customize CNTs…

When preparing molecular dynamics simulations using GROMACS, a common hurdle arises: how to define specific groups of atoms or residues for analysis, restraints, or pulling simulations. GROMACS provides a set of default index groups (such as Protein, Water, or Ions),…

If you work with molecular models, chances are you’ve run into the frustration of misaligned structures. Whether you are comparing different conformers, preparing models for visualization, or setting up simulations, having your molecules neatly organized in the coordinate space is…

Geometry optimization is one of the most crucial steps in molecular modeling. Whether you’re preparing a structure for dynamics, adjusting imported experimental data, or simply trying to understand molecular conformations better, a good cleanup process can save you both time…

When working on complex molecular systems, visualization is key. But have you ever opened a molecular model and found yourself buried under a forest of overlapping labels? Labels for every atom, residue, and molecule crowding the screen can slow down…

When working on molecular models, clarity is everything. Whether you’re preparing material for publication, sharing insight with collaborators, or simply trying to keep track of atomic measurements during a simulation, visual readability matters. In SAMSON, the ability to measure distances,…

Molecular modelers often struggle when trying to create clear and informative animations that follow the vertical structure of their systems—especially in elongated molecules or membrane environments where visual focus tends to shift along the vertical axis. If you’ve ever wished…

Choosing the right sampling region is a crucial step when exploring ligand unbinding pathways in molecular modeling. This step directly influences the direction in which the ligand is permitted to move and the quality of the unbinding paths found. In…