For many molecular modelers, running heavy simulations locally can be time-consuming and computationally expensive. That’s why cloud-based services like AlphaFold, NVIDIA BioNeMo, or GROMACS, integrated into SAMSON, have become increasingly popular. However, once your job finishes running in the cloud,…

If you’ve ever clicked a button in your molecular modeling process and instantly regretted it, you’re not alone. Trial and error is part of any design process, but in molecular modeling, mistakes can be costly—in time, in effort, and in…

When working on complex molecular models, visual clarity can make all the difference. If your structures are crowded with overlapping labels and measurements, it becomes harder to analyze your data, communicate your findings, or even stay focused. Fortunately, SAMSON provides…

When working with large biomolecular systems using GROMACS, it’s often necessary to define custom index groups—for example, to specify pull groups for umbrella sampling, analyze specific subsets of atoms, or apply restraints. But creating these groups manually using gmx make_ndx…

When visualizing molecular systems and presenting dynamics to collaborators, students, or in publications, clarity and focus matter. One subtle yet powerful tool in the molecular modeler’s toolkit is the ability to rotate a selected group of particles around its geometric…

One of the challenges structural biologists often face is not only computing and visualizing protein motions, but also saving them in a way that is easy to analyze, compare, or share with collaborators. Whether you’re studying conformational transitions or designing…