Author: OneAngstrom

For molecular modelers aiming to calculate accurate free energy profiles along reaction coordinates, Umbrella Sampling is a common go-to. But an often overlooked challenge is selecting the right set of initial conformations. Too few, and your sampling may be insufficient.…

A common bottleneck for researchers preparing molecular systems for GROMACS simulations is dealing with index groups. Whether you’re setting up umbrella sampling, defining distance restraints, or tracking domains across simulations, you often need to define custom selections beyond the standard…

When preparing molecular animations, one common challenge is to selectively emphasize particular components of a system—be it a ligand, a protein domain, or a cofactor—at specific points in time. Traditional methods might rely on changing opacity or tweaking rendering styles.…

If you’re trying to understand how a ligand might leave a protein’s binding pocket, the Ligand Path Finder app in SAMSON offers a powerful method to simulate ligand unbinding pathways. But there’s one subtle yet crucial step that can make…

One of the constant challenges faced by structural biologists and molecular modelers is trying to compare only a specific region of interest within proteins. Protein structures are big, often composed of hundreds or thousands of residues, but researchers are frequently…

Keeping track of complex molecular models can be a challenge, especially when working with large biomolecular systems or managing multiple simulation setups. Whether you’re designing a drug candidate, investigating protein-ligand interactions, or comparing molecular structures, having a clear overview and…

Adjusting atomic-level properties in molecular models often feels more complex than it should be. Whether you’re verifying atom positions, fine-tuning residue groups, or trying to undo an unexpected change, quick access to reliable attribute data is essential. This is where…

For molecular modelers working with solid-state materials, understanding and manipulating crystal structures is essential. But cutting crystals along specific directions—especially when dealing with Miller indices—can be confusing or tedious in many software environments. If you’re using SAMSON, the integrative molecular…