Author: OneAngstrom

Running cloud-based simulations for molecular modeling can save both time and computational resources, but keeping track of jobs—starting, updating, downloading results—can become overwhelming. If you often feel like your workflows are being stretched thin across tools and platforms, the Job…

When working on molecular dynamics simulations with GROMACS, ensuring reproducibility and compatibility with previous publications or validated workflows is often essential. But what if your workflow relies on a specific version of GROMACS that’s not exactly the one bundled within…

When working with protein structures from the Protein Data Bank (PDB), one common challenge is visualizing how a single asymmetric unit extends into biological assemblies or crystal lattices. These symmetry mates can be critical for understanding quaternary structures, detecting interfaces,…

Working on complex molecular systems often means juggling dozens of visualization states, selections, and scripts in SAMSON. Setting up a view, applying the right model to a ligand, or cleaning up water molecules can take up valuable time—especially when repeated…

When modeling protein conformational transitions, a common source of frustration is making sure the start and goal conformations are properly set up in the simulation environment. If these aren’t prepared correctly, everything from calculations to visualization can fail or produce…

Creating carbon nanotube (CNT) models often requires navigating parameters, scripting input files, or searching through existing structures. For molecular designers and simulation researchers, this can slow down workflow, especially when trying to design specific geometries for mechanical or transport studies.…

When you’re building animations of molecular simulations or presentations, one common experience is realizing that you’ve created a beautiful final animation—only to discover that you don’t have an exportable trajectory of the structures along the way. For many modelers, it…

Designing custom polymers often starts with building blocks: monomers. But if you’ve ever spent hours manually assembling repeat units just to test a new polymer idea, you’re not alone. Many molecular modelers face the tedious process of building polymers atom…

When working with molecular simulations in GROMACS, setting up custom index groups can be a source of both power and confusion. Many users need to define custom atom groups for pulling, restraints, or detailed analysis, but the process can feel…

Working on a molecular simulation in solution? If the system you’re modeling is approximately spherical—like a protein, micelle, or nanoparticle—you might be wasting compute time without realizing it. Let’s talk about unit cell shapes and how your choice impacts performance…