A protein structure file may show only part of the arrangement you need to study. The coordinates in front of you could represent an asymmetric unit, while symmetry information in the PDB file describes how related copies are positioned around…

A molecular simulation can be ready to run and still hit a practical limit: the system is too large for your workstation, or you need to keep your local machine available for other work. Moving a GROMACS calculation to the…

When a molecular trajectory plays, the part you want to inspect can drift toward the edge of the view—or out of it altogether. Repositioning the camera by hand can interrupt the animation and make it harder to compare motion. SAMSON’s…

A protein-docking run can produce many candidate poses, and a broad search may spend time exploring orientations that are unlikely to matter. If you already have evidence about where two proteins bind, you can use that knowledge to narrow the…

A candidate molecular pathway can be useful for seeing how a ligand might move, yet still contain awkward intermediate structures. If you already have a sequence of conformations or a path, the Parallel Nudged Elastic Band (P-NEB) app in SAMSON…

Two protein structures can show different conformations, but comparing the endpoints alone does not reveal how the molecule might move between them. For molecular modelers, building a continuous path is often the difficult next step: the structures need to be…

A molecular project can be difficult to hand off for a simple reason: the structure is only part of the work. The steps that produced a result may live in a separate script, a researcher’s notes, or a folder of…

A coarse-grained system can look ready for simulation and still run into trouble during preparation. One easily missed cause is the distance used when adding solvent. In a MARTINI model, a water bead represents several water molecules, so a default…