OneAngstrom – Page 16

Quickly Filter What You See: Controlling Molecule Visibility with NSL in SAMSON

For molecular modelers working with large and complex systems, a common challenge is visibility management: how to quickly hide or reveal molecules based on specific properties. Whether you are hunting for just the visible ligands, identifying hidden molecular chains, or…

Custom Index Groups in GROMACS: A Simple Way to Enhance Your Analysis

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If you’ve ever felt limited by default index groups when running GROMACS simulations, you’re not alone. Often, researchers require more flexibility to isolate and analyze specific parts of a system—say, alpha helices, or a specific chain of interest. Manually creating…

Avoid Rework: How to Set Up Custom Index Groups Early in Your Simulations

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When working with molecular simulations in GROMACS, little is more frustrating than realizing — mid-way through equilibration — that you forgot to define a group of atoms you need for a specific analysis or biasing method. And while GROMACS automatically…

Tired of Slow Optimizations? Try the FIRE Minimizer for Smoother Molecular Relaxation

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When preparing molecules for a simulation or cleaning up a structure after import, every molecular modeler eventually runs into the challenge of geometry optimization. Some methods are effective but slow, especially when dealing with systems undergoing large-scale collective motions. That’s…

Avoid Simulation Artifacts: How to Properly Define Your Box for COM Pulling

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One of the most common sources of simulation issues in molecular dynamics is the improper definition of the simulation box during setups involving pulling between molecular chains. This often results in unintended interactions across periodic boundaries, leading to inaccurate results…

Running AlphaFold-2 Predictions in SAMSON: Simplified Structure Modeling from FASTA Files

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Molecular modelers often face a common challenge: how to reliably predict protein structures with tools that are accessible, secure, and flexible enough to support a variety of research workflows. With the growing popularity of AlphaFold-2, the ability to make structure…

Making Molecules Appear When You Want Them To

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Controlling the visibility of elements in molecular animations can be frustrating. You might want some parts of your model to appear at specific times without gradually fading in or tweaking transparency. This is especially important in presentations or educational videos…

Making Molecules Rock: A Simple Way to Add Motion to Your Molecular Visualizations

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Visual storytelling is a powerful tool in molecular modeling, whether you’re preparing a research presentation, explaining a mechanism, or highlighting a key structural feature. Molecular animations, when done right, can reveal dynamics that a static image simply can’t capture. However,…

Drawing Nanotubes with a Drag—Fast Design in SAMSON’s Viewport

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Designing carbon nanotube (CNT) structures can be a repetitive chore for molecular modelers and nanoscientists, especially when quick iterations or small variations are needed. Using traditional parameter input forms for each tube can feel cumbersome. But if you’re working in…

A Quick Way to Minimize Entire NMR Ensembles at Once in SAMSON

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Working with NMR-derived molecular structures often means managing ensembles of conformations. But what if you need to quickly energy-minimize all conformations in one go—without messing with topology files or writing scripts? The Molecular Restrainer extension in SAMSON provides a fast…