SAMSON Blog – Page 130

Quickly Filter Conformations by Atom Count in SAMSON

When working with molecular systems in SAMSON, researchers often deal with complex models containing numerous conformations. A common challenge during analysis is identifying conformations based on specific structural features—such as the number of atoms. For instance, in simulations involving conformational…

Keeping Track of Cloud Simulations in Molecular Modeling

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Running molecular simulations in the cloud can save time and computational resources, especially when using tools like AlphaFold or GROMACS directly from SAMSON. But once you’ve launched your jobs, how do you stay organized? How do you check the progress,…

Working with Visibility Flags for Lights in SAMSON

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Managing complex molecular scenes in SAMSON can quickly become challenging when multiple lights are added for visualization. Lighting plays a crucial role in highlighting structural details, but keeping track of what’s visible — especially when debugging rendering settings — can…

A Quick Way to Build Protein Transition Paths Without Simulations

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Researchers often need to visualize or quantify conformational transitions in proteins. Whether you’re modeling domain movements, setting up umbrella sampling, or preparing steered dynamics, having a continuous path between two experimentally determined structures can save you time—and avoid launching time-consuming…

Struggling to Open Molecular Files? A Quick Guide on Adding Importers in SAMSON

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Anyone who’s worked in molecular modeling knows the moment: you’ve found the perfect structure file online — maybe a .pdb, .mmtf, or a cube file — but your software doesn’t recognize the format. It’s frustrating, especially when you’re focused on…

Running GROMACS Simulations in the Cloud, Without the Headaches

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Setting up and running molecular dynamics (MD) simulations can be time-consuming and computationally expensive, especially for large systems or long simulations. Many modelers face hardware limitations on their local machines and end up spending hours managing dependencies or queue systems…

Struggling to manage animation visibility? Here’s how NSL makes it smoother.

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When managing molecular animations in SAMSON, one common frustration is losing track of what’s visible and what’s not. You might be aligning molecular events across time, toggling components on and off for clarity, or preparing a story for presentation. But…

Cleaning Hundreds of PDB Files Doesn’t Have to Be Painful

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If you’ve ever tried to prepare dozens or even hundreds of protein structures for simulations or machine learning, you know how quickly things can become tedious. Downloading PDB files, stripping water and ions, resolving alternate locations, adding missing atoms… And…

Avoiding Selection Frustration: A Quick Guide to Node Group Attributes in SAMSON

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When working with complex molecular models, it’s common to group atoms, residues, or entire molecular structures for easier manipulation. But as models become larger, selecting and filtering node groups effectively becomes a challenge. If you’ve ever struggled to isolate just…

Avoid Simulation Headaches: Add Custom Index Groups During Equilibration or Simulation

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Preparing molecular simulations in GROMACS often involves defining specific atom groups — known as index groups — for tasks like pulling, restraints, or targeted measurements. GROMACS automatically generates standard groups (e.g., for protein, solvent, ions), which often suffice. But sometimes,…