Author: OneAngstrom

Designing complex polymers from scratch can be a rewarding yet error-prone task. A common challenge faced by molecular designers is managing repeat units (monomers) and their connections, especially when diverse bond types and large polymer chains are involved. If you’ve…

Refining protein structures can be a subtle and time-consuming process. One of the common challenges molecular modelers face is fixing residues with unfavorable conformations before running simulations. A residue that slightly deviates from a stable region in Ramachandran space can…

Creating molecular animations often involves showing or hiding specific atoms, residues, or molecular structures across time. But if you’re changing visibility in a manual, step-by-step process, it can quickly become tedious—especially if you’re trying to time these changes precisely in…

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…