Author: OneAngstrom

When setting up a coarse-grained (CG) molecular simulation, one of the most frequent stumbling blocks for modelers is improperly defined boundary conditions. A misconfigured periodic box can lead to unphysical interactions and ultimately unreliable results. In CG systems — particularly…

When molecular modelers perform virtual screening or docking of ligand libraries, one common challenge is managing and interpreting the output. The task doesn’t end with docking — in fact, that’s just the beginning. Making sense of hundreds (or thousands) of…

Running complex molecular simulations in the cloud can be a time-saver, but many molecular modelers find themselves juggling dozens of jobs without a good way to keep everything organized. Whether you’re launching protein folding simulations with AlphaFold, running molecular dynamics…

Molecular modelers and educators often face the challenge of drawing attention to specific regions of a molecule during presentations or animations. Whether you’re preparing a lecture, a publication figure, or an animation for collaboration, it’s sometimes essential to progressively hide…

When preparing molecular systems for simulation, removing water molecules is a common step. However, not all waters are useless. Some are tightly bound or located in active sites and play critical roles in structure and function. Deleting all crystal waters…

For many molecular modelers working in university labs, research facilities, or strict IT environments, installing new software can become a frustrating experience. Why? Because installing software often requires administrative privileges, meaning researchers have to wait for IT approval or assistance—a…

Running molecular dynamics (MD) simulations for a variety of protein systems often comes with a familiar headache: reproducibility and consistency across runs. 🧠 Whether you’re screening mutations, comparing homologs, or simply evaluating binding dynamics across different proteins, ensuring that all…

One of the recurring confusions among molecular modelers using GROMACS is selecting the proper input files for a production molecular dynamics (MD) simulation. This seemingly simple step can quickly become a bottleneck—especially when switching between equilibration and production phases, or…