SAMSON Blog – Page 189

Why Molecular Modelers Should Care About SAMSON Apps

Whether you are docking ligands, visualizing interactions, or performing more advanced simulations, chances are you’ve repeatedly jumped between tools that don’t quite integrate well. This friction can cost not only time but also accuracy, especially when transferring data or redoing…

When Bonds Break — and Reform: Exploring Topology Changes with IM-UFF

OneAngstrom

One common challenge in molecular modeling is smoothly editing molecular systems while maintaining physical plausibility. Modifying a structure often requires deleting and recreating bonds manually, adjusting atom types, and reconfiguring the force field setup to reflect changes. These steps can…

Quickly Identifying the Right Render Presets in Complex Molecular Scenes

OneAngstrom

When working on intricate molecular models, it’s common to juggle multiple render presets to fine-tune visuals. However, as the number of render presets grows, identifying and managing them becomes increasingly time-consuming. If you’ve ever wished there was a clearer way…

Custom Index Groups in GROMACS: A Simple Way to Target Specific Atoms and Residues

OneAngstrom

If you’ve ever run a molecular dynamics simulation using GROMACS, there’s a good chance you’ve faced this frustrating moment: you need to track say, only the side chains of neutral residues, or analyze specific atoms across your trajectory — but…

How to Quickly Find the Right Chains in Large Molecular Systems

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When working with large biomolecular systems such as proteins, nucleic acids, or molecular assemblies, finding and selecting specific chains based on their properties can be time-consuming. If you’re a molecular modeler who has ever needed to isolate chains with more…

Filtering Molecular Models by Atom Counts in SAMSON’s NSL

OneAngstrom

One of the most common challenges in molecular modeling is efficiently navigating complex models with thousands — sometimes millions — of atoms. Whether you’re comparing fragments, analyzing substructures, or scripting selections, filtering based on atom types and counts can help…

Custom Index Groups: Fine-Tune Your Simulation Setup in SAMSON

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When preparing molecular simulations with GROMACS, setting up your system with precision can save you from troubleshooting downstream. One common pain point for molecular modelers, particularly when dealing with analysis or advanced simulation protocols like umbrella sampling and pulling experiments,…

Cleaning Multiple PDB Files Without the Chaos

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Anyone who’s worked with protein structures knows the routine: download a dozen PDB files, clean each one manually, and try not to make mistakes along the way. It’s tedious—and it’s easy to overlook a missing hydrogen or a dangling ion.…

Rewinding Molecular Trajectories: A Closer Look at the ‘Play Reverse Path’ Feature in SAMSON

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When studying molecular systems, a common task is to analyze how a structure evolves over time. Equally essential is the ability to retrace and visualize these changes backwards—whether to better understand conformational transitions, double-check simulations, or prepare smooth looping animations…

Making light nodes appear or disappear in SAMSON with visibility flags

OneAngstrom

Molecular modelers working with complex scenes often need to manage multiple light sources to optimize visual renderings. However, coordinating which lights are actually displayed in a rendered view—without deleting or restructuring the scene—can be tricky. What if you just want…