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…

When preparing coarse-grained molecular dynamics (MD) simulations with GROMACS, many users encounter an unexpected obstacle: solvent molecules too close to the solute. This typically results in unrealistic overlaps and density artifacts that force them to redo the setup or troubleshoot…

If you’ve ever spent valuable minutes reselecting the same parts of a molecular system over and over again during analysis or visualization, you’re not alone. Molecular modeling often requires switching focus between a ligand and its receptor, or zooming in…

When setting up covalent docking simulations, one of the most frequent and frustrating sources of error is neglecting to properly define the chemical structure of the ligand—especially if the ligand comes from a crystal structure where it is already covalently…