When setting up molecular dynamics simulations for a series of molecular conformations, choosing the right periodic box parameters can lead to more efficient simulations and better results. In SAMSON’s GROMACS Wizard, users working with multiple conformations have two main options…

For researchers using GROMACS, setting up pulling simulations often requires creating custom index groups—say, to specify exactly which atoms or chains to pull. But writing index groups by hand in GROMACS can be awkward, especially when you’re dealing with complex…

Have you ever wanted to try out a new analysis workflow but hesitated because setting everything up from scratch seemed daunting? If you’re exploring how to predict protein-ligand complexes using NMR data, there’s a helpful shortcut in SAMSON worth knowing:…

When creating molecular animations in SAMSON, it’s common to spend time carefully orienting the scene to show a particular structure or interaction. But if you don’t explicitly control the camera during all frames, SAMSON might change the viewpoint midway as…

Creating compelling molecular animations can be surprisingly tedious, especially when presenting multi-component systems. A common challenge in structural bioinformatics and molecular modeling is illustrating how different components relate spatially in a complex supramolecular assembly. Whether it’s for teaching, a publication,…

When performing protein-protein docking, modelers often face a critical tradeoff: how to balance docking accuracy with efficient computation. Complex systems can take hours to dock, especially if you’re exploring the full 3D orientation space of the ligand relative to the…

If you’ve ever had to prepare multiple protein structures for docking, simulations, or other modeling tasks, you know how tedious and error-prone it can become. Opening each file, fixing alternate atom locations, removing waters or cofactors, checking for missing atoms—it’s…

When working with complex molecular systems, it can be challenging to keep track of atoms, residues, and structural regions – especially when they’re rendered as a sea of spheres and sticks. If you’ve ever found yourself squinting at your molecular…