If you’re working with molecular dynamics simulations, chances are you’ve used GROMACS, a powerful and widely used MD engine. SAMSON’s GROMACS Wizard makes it easy to run GROMACS computations, both locally and in the cloud. But what if you need…

Running a molecular dynamics (MD) simulation is only half the story. For many molecular modelers, the real challenge comes after: importing the results, making sense of them, and preparing overview plots to check simulation health or communicate findings. If you’ve…

When working with protein structures from the Protein Data Bank (PDB), modeling biological assemblies usually requires rebuilding symmetry-related units based on transformation matrices encoded in the structure file. This can often be a tedious task — and yet it’s essential:…

Energy minimization is a critical step in preparing molecular systems for simulations, ensuring that your model is stable and ready for further refinement. But for many molecular modelers, especially those working with personal computers, a common problem arises: How do…

Have you ever spent hours building a beautiful molecular model, only to find that the final visualization feels… flat? You’re not alone. Molecular structures are inherently three-dimensional, but without the right rendering techniques, their depth can get lost on screen.…

Running cloud-based simulations for molecular modeling can save both time and computational resources, but keeping track of jobs—starting, updating, downloading results—can become overwhelming. If you often feel like your workflows are being stretched thin across tools and platforms, the Job…

When working on molecular dynamics simulations with GROMACS, ensuring reproducibility and compatibility with previous publications or validated workflows is often essential. But what if your workflow relies on a specific version of GROMACS that’s not exactly the one bundled within…

When working with protein structures from the Protein Data Bank (PDB), one common challenge is visualizing how a single asymmetric unit extends into biological assemblies or crystal lattices. These symmetry mates can be critical for understanding quaternary structures, detecting interfaces,…

Working on complex molecular systems often means juggling dozens of visualization states, selections, and scripts in SAMSON. Setting up a view, applying the right model to a ligand, or cleaning up water molecules can take up valuable time—especially when repeated…