SAMSON Blog – Page 146

Running your own GROMACS version in SAMSON without breaking a sweat

Running molecular dynamics simulations with GROMACS? If you’ve ever needed to use a specific version of GROMACS (perhaps for reproducibility, GPU support, or compatibility with certain force fields), you know how frustrating it can be to tie everything together smoothly—especially…

Editing Bonds and Atom Types on the Fly in SAMSON’s UFF Simulator

OneAngstrom

When working with molecular models, manually tuning atom types and bond orders can feel like a tedious and error-prone process. But sometimes, automatic perception just doesn’t cut it—especially when you’re dealing with complex or unusual molecules. If you’ve ever wanted…

Making smarter selections with node group attributes in SAMSON

OneAngstrom

For molecular modelers working with large systems—be it proteins, materials, or supramolecular complexes—managing selections efficiently can significantly improve productivity and reduce errors. In SAMSON, the Node Specification Language (NSL) introduces a powerful way to target specific parts of your model…

Feeling Lost in Molecular Modeling Software? Try Learning by Doing

OneAngstrom

Many molecular modelers, whether beginners or experienced researchers switching to new tools, face a common challenge: getting started quickly and effectively. Dense documentation, unfamiliar interfaces, and unclear workflows often delay productivity and increase frustration. If this rings a bell, you’re…

Why Only One Editor Can Be Active in SAMSON—and Why That’s a Good Thing

OneAngstrom

If you’ve used SAMSON to design or manipulate molecular models, you’ve likely come across the concept of editors. These tools power an essential aspect of your modeling experience: they make things happen when you interact with atoms, molecules, or entire…

Why Your SAMSON Extension Won’t Load (And How to Fix It)

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If you’ve built a SAMSON Extension and it suddenly won’t load when you start SAMSON, you’re not alone. One of the most common issues developers and users stumble upon is version incompatibility between the Extension and the SAMSON SDK. It…

Avoid Pathway Artifacts: How to Properly Set Up Your Protein System in SAMSON

OneAngstrom

One of the most common sources of error when exploring conformational transitions in proteins is an incorrectly prepared system. Structural inconsistencies, missing atoms, or mismatched residue numbering can not only cause software crashes but generate misleading results when modeling pathways.…

Making Selections Work for You: Filtering Render Presets in SAMSON with NSL

OneAngstrom

When working in molecular design and visualization, it’s easy to accumulate multiple render presets while experimenting with colors, styles, and representations. But what if you’re revisiting a project weeks later—or collaborating with others—and need to quickly find a specific render…

Selecting Atoms by Geometry in SAMSON

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In molecular modeling, selecting the right set of atoms can be the difference between getting a meaningful result and spending hours troubleshooting. One common requirement is to select atoms based on their molecular geometry—for example, tetrahedral or trigonal planar geometries.…

Avoiding Equilibration Errors in GROMACS Wizard: How to Handle Input Files in NPT Equilibration

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When preparing molecular dynamics simulations, one of the most common sources of confusion is choosing the correct input for each stage of the simulation pipeline. This is especially true when transitioning between the NVT and NPT equilibration steps. If the…