OneAngstrom – Page 306

Quickly Find Molecules with Specific Features in SAMSON Using NSL

One common need for molecular modelers working with complex systems is to quickly identify and select molecules with particular properties — such as those with a high number of atoms, a specific charge, or visibility status. Finding such molecules manually…

Avoid Artifacts: Make Sure Your Protein is Properly Minimized

OneAngstrom

Unexpected distortions in protein simulations can often be traced back to one common oversight: skipping energy minimization before transition path planning. Whether you’re exploring conformational transitions or generating intermediate structures between known states, minimizing your system ensures your results are…

Quick Adjustments, Big Impact: Customizing GROMACS Parameters in SAMSON

OneAngstrom

Running molecular dynamics simulations often involves fine-tuning a complex set of parameters. Whether you’re optimizing for performance or adapting to a specific research protocol, manually editing a GROMACS .mdp file can be tedious and error-prone—especially when trying to track which…

Filtering Conformations by Atom Count in SAMSON

OneAngstrom

When working with molecular conformations, size matters — especially when you’re exploring large datasets or designing simulations with molecules of specific complexity. If you’re a molecular modeler using SAMSON, selecting conformations based on the number of atoms can help you…

Finding Your View: A Practical Guide to SAMSON’s Camera Attributes

OneAngstrom

When working with complex molecular systems in SAMSON, one common source of frustration is trying to efficiently manage and return to specific viewpoints. Whether you’re preparing publication-ready visualizations or comparing structural motifs across different conformations, being able to name, select,…

Avoiding Compatibility Headaches: Understanding SAMSON’s Versioning Scheme

OneAngstrom

When working on complex molecular modeling projects, maintaining compatibility across different software versions can become a real challenge—especially when collaboration is involved. Files that work on one computer may refuse to open on another due to subtle version mismatches. This…

Same or unique box sizes? A practical look at periodic box setup for batch MD in SAMSON

OneAngstrom

When preparing a molecular dynamics (MD) simulation, defining the periodic box correctly ensures accuracy and stability in the results. But what happens when you’re not just simulating one structure, but a whole batch of conformations? Should each snapshot have a…

Avoid Common Docking Issues: Preparing Ligands Properly in SAMSON

OneAngstrom

One commonly overlooked yet crucial step in molecular docking studies is ligand preparation. 🧪 Docking algorithms like AutoDock Vina assume that ligands are clean, chemically sensible, and ready to interact with the target. Unfortunately, that’s not always the case —…

Quickly Hide or Show Animations in SAMSON Without Clicking Around

OneAngstrom

In molecular modeling, especially when working with complex systems or animations, user interfaces packed with many nodes can quickly become overwhelming. It’s sometimes surprisingly hard to focus on what really matters—perhaps a specific ligand interaction or a folding mechanism—when multiple…

Position Restraints During NPT Equilibration: What They Are and Why They Matter

OneAngstrom

When preparing a molecular system for simulation, understanding the role of position restraints during the NPT (constant pressure and temperature) equilibration phase can save you time—and help you avoid unexpected behavior in your trajectories. This post walks you through how…