OneAngstrom – Page 174

Are Your Pull Simulations Too Tight? How to Set Up a Proper Simulation Box for COM Pulling in GROMACS

When performing molecular dynamics simulations involving center-of-mass (COM) pulling, failing to correctly define the simulation box can lead to artifacts—especially when periodic boundary conditions come into play. One common challenge molecular modelers face is ensuring that enough space exists in…

A Simple Way to Animate Molecular Docking in SAMSON

OneAngstrom

If you’ve ever prepared a molecular presentation and wanted to clearly show a ligand docking into a receptor, you may have run into a common challenge: animating the motion in an intuitive, visually appealing way—without spending hours tweaking coordinates or…

Targeting Residues by Charge and Polarity in SAMSON

OneAngstrom

One common challenge in molecular modeling is efficiently locating specific types of residues based on their physicochemical properties. For example, you might want to highlight all positively charged residues in a protein to identify likely binding sites for negatively charged…

Understanding FIRE Minimizer Settings in Molecular Simulations

OneAngstrom

When working with molecular models, one common step before running simulations or analyses is geometry optimization. This ensures that your structure starts from a relaxed configuration, typically corresponding to a local energy minimum. In SAMSON, an integrative platform for molecular…

Why Your SAMSON Extension May Not Load—and How to Fix It

OneAngstrom

It’s a familiar and often frustrating situation in molecular modeling platforms: you launch your software, expecting your favorite extension to be readily available—only to find it missing or non-functional. If you use SAMSON, there’s a good chance this is caused…

A Practical Guide to Editing Dihedral Angles in SAMSON

OneAngstrom

Manipulating dihedral angles is a common task in molecular modeling, especially when preparing conformational ensembles, exploring molecular flexibility, or setting up simulations. For many scientists, this operation can be cumbersome and tedious in overly complex or rigid software interfaces. In…

Making Molecule Libraries Fast with Fragment Replacement in SAMSON

OneAngstrom

Creating libraries of related molecules is a key step in modern drug design and materials science. For molecular modelers, manually generating chemical variants by editing structures can be time-consuming and error-prone. What if you could instantly generate hundreds of structural…

Smooth Transitions in Molecular Presentations: Setting Backgrounds in SAMSON

OneAngstrom

Molecular modelers often face a challenge when preparing presentations: how to keep the audience focused on key structures and transitions, without overwhelming them with static, jarring slides. Smooth visual transitions help maintain engagement and highlight structural dynamics at just the…

Solving Visibility Overload: Use the Disappear Animation to Focus on What Matters

OneAngstrom

When working with complex molecular systems, it’s easy to get lost in a sea of atoms, bonds, labels, and models. Whether you’re crafting a presentation for a paper or a visualization for teaching, clarity is key. One common pain point…

Easier Molecular Flythroughs with Horizontal Camera Moves

OneAngstrom

Creating smooth molecular flythroughs can be a real challenge, especially when you’re trying to guide viewers along a complex structure without disorienting them. Whether you’re preparing a video for a publication, a presentation, or educational content, camera transitions matter. One…