Author: OneAngstrom

One common challenge for molecular modelers working with GROMACS is dealing with long-running energy minimization calculations. These simulations can temporarily block workflow, especially when computational resources are limited. Fortunately, the SAMSON GROMACS Wizard has integrated local job management capabilities that…

As molecular modelers, we often rely on labels to communicate the identity, location, or properties of atoms, residues, and molecules in our models. Whether you’re preparing publication-quality images or simply organizing your project, clear labeling is key. But if you’ve…

If you work with protein-ligand docking, molecular dynamics, or virtual screening, you’ve probably faced the time-consuming chore of preparing dozens—or hundreds—of protein structures. From removing unwanted molecules to adding missing atoms, the process can quickly become a bottleneck. That’s where…

When working on molecular modeling projects, things can get complex very quickly. Trying to manage multiple molecules, simulation settings, scripts, and custom data often leads to workflows spread across different tools, folders, or even computers. This fragmentation can cause confusion…

Sometimes the latest software update isn’t the best solution for everyone. Whether you’re continuing a project that depends on a previous version or need compatibility with specific SAMSON Extensions, installing an older version of SAMSON can be necessary and even…

When preparing molecular animations, one common challenge is drawing attention to specific parts of a model without overwhelming the viewer with too much motion or information. Whether you’re highlighting a binding event, a structural change, or just toggling visibility for…

Whether you’re preparing a molecular presentation, creating a scientific animation, or designing an educational video, selectively hiding parts of your molecular model can be essential. Highlighting only the key actors of a protein-ligand interaction, demonstrating intermediate stages of a conformational…

If you’ve ever had to run a Molecular Dynamics (MD) simulation for more than one conformation of a molecule, you’ve probably felt the pain of repetition: preparing each system individually, applying the same settings again and again, and tracking multiple…

One of the recurring challenges in molecular modeling is checking whether a protein structure is physically plausible before running simulations or using it in predictive workflows. A common issue: residues with unfavorable backbone conformations can skew simulations, especially in homology…

When creating molecular animations, clarity is everything. Whether you’re preparing a presentation, designing teaching materials, or just trying to isolate a part of your model, hiding atomic structures at the right frame can make a big difference in storytelling and…