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…

Designing polymers with specific repeating units—especially when bond types matter—is a common challenge for molecular modelers working on materials science, drug delivery, or bioengineering applications. While small molecules can be drawn fairly quickly, building realistic polymer sequences with chemically accurate…

One common frustration in molecular modeling workflows is ensuring that simulations are reproducible and compatible with local computing environments. Especially for researchers fine-tuning their systems or working in highly specialized setups, using a customized version of GROMACS instead of the…