Author: OneAngstrom

Anyone who has worked with protein structures knows the feeling: you download hundreds of PDB files for computational modeling, but before you can even run a simulation or docking, you need to clean them. Hydrogens missing. Water molecules everywhere. Ligands…

For many molecular modelers, the steep learning curve of new platforms can be a major barrier to getting started. Traditional manuals and video tutorials are often non-interactive and require switching back and forth between the tool and the guide. This…

Running molecular simulations at the scale of full biological assemblies can be time-consuming and computationally intensive. But often, nature provides a shortcut: symmetry. If your system has symmetry, you might not need to simulate the entire structure. Instead, you can…

Preparing a molecular model for simulation often involves an essential but sometimes time-consuming step: geometry optimization. When atoms are not in energetically favorable positions, your simulation might diverge or waste computational resources on fixing geometry-related problems. Enter the FIRE Minimizer,…

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…