Running production molecular dynamics (MD) simulations can very quickly turn into a juggling act for molecular modelers: multiple files, simulation logs, and trajectories all need to be carefully tracked. If you’re running several simulations — maybe testing different parameters, different…

When you’re preparing a molecular presentation—whether for a class, a paper, or a conference—one of the biggest challenges is guiding your audience’s attention. Just like in film, controlling the camera is what allows you to tell a coherent and visually…

Water is everywhere in biological systems, but when it comes to preparing a protein structure for simulations in GROMACS, not all water molecules need to stay. In fact, a common challenge faced by molecular modelers is identifying and removing only…

When simulating molecular systems, researchers often need to model multiple copies—or replicas—of the same protein. This is especially relevant for studying concentration effects, protein aggregation, or large-scale interactions. But generating coarse-grained (CG) models for these replicas can become a tedious…

When studying molecular dynamics (MD) simulations of protein-ligand complexes, one common challenge is interpreting how a ligand moves during a binding or unbinding event. Especially in crowded systems or long trajectories, it can be hard to get a clear picture…

When designing new molecules through analogue generation, one of the key challenges is identifying where to modify your existing structure in a systematic and meaningful way. Whether you’re exploring structure-activity relationships or trying to improve target binding, specifying the right…

One of the most common frustrations among molecular modelers is spending time repeatedly adjusting visualization settings to highlight the same structural regions—receptors, ligands, water molecules—across different molecular systems. Color schemes, visual styles, atom selections… it can all become time-consuming and…