One of the most common stumbling blocks for molecular modelers performing simulations with GROMACS is ensuring that their system is properly equilibrated at the right temperature before production runs. Jumping into molecular dynamics without this step can lead to unphysical…

When presenting molecular mechanisms, one challenge researchers often face is how to draw attention to key events or components without overwhelming the viewer with too much visual information. Whether it’s emphasizing a cofactor binding, a sudden conformational change, or the…

One common challenge in molecular modeling is modifying molecular structures on the fly—connecting or breaking bonds—without having to recalculate everything from scratch. Typically, simulations require a fixed topology, and making any structural change leads to restarting your workflow, setting parameters…

Protein docking can be time-consuming, especially when predictions yield a large number of unlikely conformations. One of the most common frustrations for molecular modelers is spending hours sorting through thousands of docking results only to end up discarding most due…

When performing molecular modeling, there are moments when a single distance or angle carries more meaning than lines of code. Whether you’re comparing bond lengths between minimized geometries, analyzing conformational changes, or just trying to keep track of a torsion…

Protein alignments play a crucial role in structure-based molecular design, helping researchers uncover conserved regions, highlight conformational differences between homologs, and guide homology modeling. But what happens when you’re only interested in a specific part of the protein? That’s a…

Accurately selecting residues in complex molecular systems is a common pain for molecular modelers. Working with large structures—especially proteins with multiple chains—can quickly become a tedious task when manual selection is spread across multiple interfaces. If you’ve ever found yourself…