Author: OneAngstrom

One of the biggest hurdles faced by researchers and students new to molecular modeling is learning how to effectively use complex software interfaces and tools. Software like SAMSON can be extremely powerful, but its wide range of features can be…

When preparing a molecular system for simulation, one of the recurring challenges is deciding what to keep and what to discard. And if you’ve worked with PDB files, you’ve likely faced the dilemma around crystallographic water molecules. Do you delete…

After going through the steps of energy minimization in molecular dynamics, it’s tempting to jump straight to equilibration and production runs. But wait — how do you know your energy minimization was successful? Many molecular modelers overlook this crucial verification…

When creating molecular animations, one challenge that frequently arises is the need to visually isolate motion. Suppose you’re showcasing how a drug docks into a protein’s binding site, and you want only the ligand to move — not the entire…

Designing molecular nanotubes is a common task in areas like nanotechnology, materials engineering, and molecular simulation. But constructing nanotubes atom-by-atom is tedious and prone to alignment issues. The good news? If you’re using SAMSON, there’s now an intuitive way to…

When exploring ligand unbinding mechanisms in protein-ligand systems, one of the most frequent sources of confusion comes from setting up the proper energy evaluation models. If your energy calculations are mismatched or incomplete, it can stop meaningful trajectory generation altogether—or…

Atom-level editing is central to molecular modeling, yet it’s often tedious to isolate subsets of atoms based on spatial and chemical criteria. Typical visual selection tools can become limiting when working with large structures or when precision is required. If…

When building molecular presentations or demonstrating molecular processes, it’s often critical to preserve how specific atoms move over time. This is especially relevant if you’re simulating docking, assembling models, or animating conformational changes. But how do you make sure that…