Author: OneAngstrom

Running molecular dynamics (MD) simulations, especially on large biomolecular systems, often pushes the limits of a researcher’s local hardware. If you’ve ever faced crashes due to memory overload or critical slowdowns on NVT or NPT equilibrations, you’re not alone. This…

One common frustration molecular modelers face when creating animations is trying to zoom into a specific region of a molecular system without altering the focus or perspective too much. Whether preparing a talk, tutorial, or research video, maintaining consistency and…

Visualizing molecular dynamics can be complex, especially when presenting ligand-receptor interactions to collaborators or students. A common challenge for molecular modelers is how to clearly and convincingly show a ligand leaving its binding site, without manually specifying precise atomic trajectories.…

Creating custom index groups in GROMACS can be a useful—and at times necessary—part of your molecular simulation workflow. Whether you’re running umbrella sampling, tracking interactions, or preparing for free energy calculations, identifying just the right atoms or residues can save…

Small configuration choices can significantly influence the results of molecular simulations. One such setting in SAMSON, when using the Universal Force Field (UFF), is the checkbox labeled Use existing bonds. Knowing when to activate it saves time and helps prevent…

When presenting molecular animations, timing is often just as important as content. Whether you’re building a video presentation for a conference, teaching molecular dynamics in a classroom, or showcasing your latest protein-ligand interaction, being able to emphasize key moments can…

Running molecular dynamics simulations with GROMACS? If you’ve ever needed to use a specific version of GROMACS (perhaps for reproducibility, GPU support, or compatibility with certain force fields), you know how frustrating it can be to tie everything together smoothly—especially…

When working with molecular models, manually tuning atom types and bond orders can feel like a tedious and error-prone process. But sometimes, automatic perception just doesn’t cut it—especially when you’re dealing with complex or unusual molecules. If you’ve ever wanted…