OneAngstrom – Page 9

Selecting atoms with natural language in SAMSON AI

Molecular modeling involves frequent selection of specific atoms, residues, chains, ligands, or binding sites. This task can become tedious and error-prone, especially in complex molecular systems. Traditional selection tools involve dropdowns, checkboxes, or writing selection syntax. Not only does this…

Quickly Identify Bonds by Type in Your Molecular Models

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When working with complex molecular structures, it’s often necessary to inspect or refine specific bond types, such as identifying only the aromatic bonds in a protein-ligand complex or checking for unusual bond patterns in generated conformers. This task, usually time-consuming…

Watching the SARS-CoV-2 Spike Move: A Useful Trajectory for Molecular Modelers

OneAngstrom

Modeling conformational changes in large biomolecular assemblies is a recurring challenge in structural biology and drug design. One protein that drew intense focus is the SARS-CoV-2 spike, which transitions between closed and open states to interact with the ACE2 receptor.…

Why You Can Only Use One Editor at a Time in SAMSON

OneAngstrom

While working on molecular models, users often wish to interact with structures in more than one way—perhaps selecting atoms, applying transformations, and generating nanostructures all in succession. In SAMSON, this flexibility is achieved through Editors: tools designed to help you…

Avoid Solvent Clashes in GROMACS CG Simulations with One Simple Tweak

OneAngstrom

When setting up coarse-grained (CG) molecular dynamics (MD) simulations in GROMACS using the MARTINI force field, one of the most common frustrations is solvent clashes. These issues often arise not from user error, but from a default behavior: GROMACS applies…

Filtering Side Chains by Atom Counts with NSL

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When working on structure-based drug design or biomolecular modeling, it’s often necessary to filter or classify molecules based on the properties of their components. For example, identifying side chains with a particular number of carbon atoms, or selecting only those…

Exporting DNA Nanostructures for Simulation with Adenita

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Running DNA nanostructure simulations can be a powerful way to test your designs before heading to the lab. But exporting complex DNA models for use in simulation tools like oxDNA can feel like a hurdle—especially when dealing with 3D nanostructures…

A Simple Way to Record Molecular Motion Without Coding

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Tracking how molecules move during simulations or interactive presentations can be key when communicating your discoveries. But if you’ve ever tried capturing atom trajectories while modifying structures in real-time—be it docking ligands, assembling molecules, or simulating dynamics—you might know how…

Reclaim Your Interface: Customizing SAMSON the Way You Work

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One of the most common frustrations for molecular modelers—and scientists in general—is spending too much time navigating software interfaces that don’t adapt to individual workflows. When every second counts in a simulation or a modeling task, toggling between windows or…

Running GROMACS Simulations in the Cloud Without Configuration Stress

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Running molecular dynamics (MD) simulations with GROMACS usually requires not just scientific knowledge, but also technical setup: compiling software, configuring command-line commands, managing dependencies, and securing enough computing resources. This can be a challenge — especially when you just want…