When working on complex molecular systems, it often happens that you want to optimize only a specific part of a molecule—perhaps just a side chain, a functional group, or a distorted region—without disturbing the rest of the structure. This is…

When working with complex biomolecular systems, labels are powerful tools. Whether highlighting residues of interest, displaying atomic distances, or tracking a subset of molecules, well-placed labels bring clarity. But when zooming in and out of large systems, things can quickly…

In molecular modeling, creating compelling and instructive animations often means clearly highlighting key interactions or transformations—without distracting motion in other areas. Ever tried to animate a docking event only to find unrelated atoms drifting around, distorting the focus of your…

When preparing a biomolecular system for simulation in GROMACS, one often encounters the need to remove water molecules — typically those originating from crystal structures in the Protein Data Bank (PDB). In many cases, however, not all water molecules should…

Biological assemblies—like protein complexes or viral capsids—often exhibit beautiful symmetry, which can be more than just aesthetic. Understanding and using this symmetry is essential in many molecular modeling workflows: from reducing computational cost to designing symmetric mutations. That said, if…

When designing analogs of a molecule in a hit optimization campaign, it’s common to work primarily with 2D molecular structures. But eventually, structural biologists and molecular modelers face an essential question: how do these analogs behave in 3D? Understanding spatial…

For molecular modelers running multiple simulations on variants of the same system—perhaps different conformations, docking poses, or even frames of an animation—preparing separate GROMACS input files manually can become repetitive and time-consuming. If you’ve been through the cycle of setting…

One common pain point for molecular modelers is discovering—too late—that a simulation fails because of issues in the structural model. Whether you’re preparing a protein-ligand complex or simulating a structure fetched from a public database, overlooked details like alternate locations,…

When visualizing molecular dynamics simulations or comparing conformational pathways, it’s often useful to view both forward and reverse directions of a molecular journey. If you’re using SAMSON, the Play reverse path animation offers a simple yet effective way to achieve…