Author: OneAngstrom

Running molecular simulations in the cloud can be an efficient way to access high-performance computing resources, but staying organized and in control of your calculations is another matter entirely. If you’ve ever struggled to manage multiple job states, find your…

When working on complex molecular models, clear and informative labeling is essential. But what happens when your scene becomes crowded, or when you zoom in and out frequently to explore different scales of your system? With SAMSON, labels can be…

Molecular modelers often generate complex trajectories—whether from structural transitions, docking analyses or dynamics—but presenting these transitions clearly can be difficult. Communicating results, sharing insights with colleagues, or documenting a simulation’s progress often demands more than static images. This is where…

Creating compelling and clear scientific visuals can be a challenge for molecular modelers. Whether you’re preparing a presentation, sharing your latest findings, or teaching students about molecular structures, you want your audience to understand the spatial arrangement of atoms—without needing…

One of the first tasks after building or importing a molecular structure is preparing it for simulation. But here’s a common dilemma faced by many molecular modelers: the geometry looks mostly correct, there are only subtle non-idealities, but running a…

When setting up molecular dynamics simulations with periodic boundary conditions in GROMACS, one of the first steps is defining the unit cell shape. This decision directly affects the computational efficiency of your simulation and how well it reflects your system’s…

When creating molecular animations, clarity of movement can often make or break your visualizations. A common challenge faced by molecular modelers and educators is how to move both the camera and its focal point vertically through a scene without distorting…

When fine-tuning a molecular dynamics workflow, being able to define your own atom groups — for pulling, analysis, or restraints — is incredibly important. GROMACS nudges you in the right direction by generating standard index groups automatically, such as Protein,…

When working on optimizing small molecules for better binding affinity or selectivity, one often faces the question: What happens if I replace or attach something at this position? Trial-and-error can be time-consuming, and manual modifications in 3D editors are prone…

When presenting molecular models—whether in research talks, educational content, or collaborative reviews—clarity is key. A common hurdle in visual storytelling is how to draw attention to important structures without cluttering the scene or drowning your audience in static visuals. This…