If you’ve ever spent an afternoon adjusting representations, tweaking color schemes, and hiding unwanted atoms just to get a single static image of your molecular system that looks the way you want — you’re not alone. Molecular modelers often face…

For molecular modelers working with GROMACS, reproducibility and performance can sometimes be at odds. Perhaps you’ve validated a workflow using a specific GROMACS build, or maybe you’ve fine-tuned your installation with particular optimizations for your hardware. But what happens when…

When modeling ligand unbinding pathways in protein systems, small oversights can lead to big blind spots — literally. One of the most frequent and easy-to-make mistakes is misdefining the sampling region, also known as the sampling box. Fortunately, SAMSON’s Ligand…

When preparing presentations of molecular structures, researchers often face the challenge of showing complex architectures and interactions in a way that is visually clear, scientifically accurate, and engaging for a broad audience. Static snapshots may suffice for publications, but they…

When creating molecular presentations or animations, timing is everything 🕒. Whether you’re preparing a communication video, building an educational resource, or capturing a memorable moment in a simulation, one pain point many molecular modelers face is how to reveal parts…

When modeling structural transitions in proteins, especially for simulations like umbrella sampling or transition path analysis, one recurring challenge for researchers is the correct import and preparation of starting and target conformations. Even minor misalignments, alternate locations, or extraneous molecules…

When preparing a molecular docking project, many researchers focus on the setup of the receptor, defining the search space, or choosing the scoring function. One critical but sometimes overlooked step is the minimization of ligands before docking. Neglecting this can…

If you’ve ever found yourself scratching your head because your molecular dynamics simulation didn’t behave as expected during the NVT equilibration phase, you’re not alone. One of the most common causes? Incorrect or inconsistent input files. Choosing the correct starting…