OneAngstrom – Page 139

A Quick Way to Build Protein Transition Paths Without Simulations

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

OneAngstrom

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

OneAngstrom

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.

OneAngstrom

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

OneAngstrom

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,…

Why Molecular Modelers Should Claim Their SAMSON Profile (And How to Make It Shine)

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When collaborating with teams or sharing your molecular modeling work with the broader community, how you present yourself online matters just as much as the quality of your research. For users of SAMSON, the integrative molecular design platform, a customizable…

Avoid Ligand Confusion: Correctly Selecting Ligand Atoms in Ligand Path Finder

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One of the most common setup issues encountered by molecular modelers working on protein-ligand interactions is an incorrect definition of the ligand itself. This can lead to inaccurate path predictions, unexpected energies, and even failure of the algorithm to find…

A Simple Way to Play Trajectories in Reverse with SAMSON

OneAngstrom

When analyzing molecular structures and motions, it’s often helpful to step back—literally. While forward trajectories offer valuable insights, playing molecular paths in reverse can highlight subtle interactions, simplify comparisons, or illustrate transitions between conformations more clearly. This is especially useful…