OneAngstrom – SAMSON Blog

Need atoms to stay put during animations? Here’s how

When animating molecular systems, one recurring challenge is showcasing a specific motion—say, a ligand docking or a protein conformational change—while keeping a subset of atoms still. If some atoms move when they shouldn’t, it can confuse viewers and diminish the…

Not Getting Your SAMSON Confirmation Email? Here’s What to Know

OneAngstrom

Registering on SAMSON Connect is the first step toward accessing powerful tools for integrative molecular design. But what if you’ve signed up and the confirmation email is nowhere to be found? For many users—especially those using Gmail—this delay can feel…

Making molecular unbinding animations easier with the Undock effect

OneAngstrom

Communicating molecular interactions doesn’t stop at showing static structures. For molecular modelers trying to convey how ligands unbind or how complex molecular assemblies disintegrate, producing clear, dynamic visualizations can become critical—especially in presentations, publications, and educational settings. One common challenge…

Eliminating guesswork: how to search by bond length in SAMSON

OneAngstrom

As a molecular modeler, you’ve probably faced the challenge of identifying parts of a molecule where bond lengths deviate from expected values. Whether you’re validating experimental data, optimizing geometries, or preparing a simulation, being able to quickly locate and filter…

Fade Objects Into View: A Clearer Way to Animate Molecular Models

OneAngstrom

When creating molecular animations, one of the biggest challenges is guiding viewer attention without overwhelming or distracting them. Whether you’re presenting a protein assembly or visualizing molecular interactions, clarity is key. That’s where the Appear animation effect in SAMSON can…

Avoiding Setup Errors: Choosing the Right Input for NVT Equilibration in SAMSON

OneAngstrom

Before any molecular dynamics simulation can begin, one crucial step stands in the way: preparing the input files properly. For many researchers working with GROMACS in SAMSON, one common source of frustration is figuring out what input the NVT Equilibration…

Selecting Molecular Segments by Atom Counts, Charges and More in SAMSON

OneAngstrom

When working with large molecular systems, filtering specific parts of the model becomes crucial to speed up workflows and improve clarity. For example, you might want to focus only on segments with a large number of atoms or a particular…

Custom Parameters in GROMACS Simulations: What You Can Control (and How)

OneAngstrom

If you’ve ever run molecular dynamics simulations using GROMACS, you’ve likely encountered the long list of options in MDP (Molecular Dynamics Parameters) files. From integrators to thermostats, every choice influences your results, and getting all of them just right isn’t…

Separate Molecular Groups Visually with the Undock Animation in SAMSON

OneAngstrom

When preparing molecular presentations or exploring molecular complexes, molecular modelers often face the challenge of clearly visualizing how different molecular groups interact — or separate. Whether it’s for highlighting binding interactions, presenting docking results, or explaining receptor-ligand dynamics, it helps…

Revealing Molecular Depth: How Ambient Occlusion Enhances Visual Clarity in SAMSON

OneAngstrom

Understanding the three-dimensional structure of molecules is critical in molecular modeling and design. However, even with powerful visualization tools, complex molecular models can sometimes feel surprisingly flat on screen. This visual ambiguity hinders structural interpretation, especially in densely packed biomolecular…