When presenting molecular systems, clarity is key. Whether you are illustrating a dynamic interaction or simply emphasizing a structural element, controlling what appears at which time can dramatically improve your viewers’ understanding. That’s where the Flash animation effect in SAMSON…

For many molecular modelers, installing and configuring GROMACS — especially with specific compiler flags, MPI settings, or GPU configurations — is a significant hurdle. It can take hours or even days to get everything working properly and reproducibly across different…

Presenting molecular systems clearly and beautifully is a constant task for molecular scientists and modelers. But manually configuring colors, styles, and rendering effects for every scene can take time—especially during presentations, teaching, or when sharing data with collaborators. If you’ve…

Running coarse-grained (CG) simulations of biomolecules often requires building systems with multiple copies of the same protein. Whether you’re simulating crowded cellular environments or studying aggregation processes, creating and managing these replicas correctly can be time-consuming and error-prone. Fortunately, SAMSON…

When running molecular simulations with GROMACS, index groups play a key role in defining subsets of your system for analysis or simulation tasks. While GROMACS creates standard groups automatically—like Protein, Water, and Ions—there are many situations where custom groups are…

If you’ve ever had to run the same molecular dynamics protocol across a set of conformations for a single molecule, you know how tedious it can be to duplicate setup steps, adjust box sizes, or ensure that each conformation is…

Creating molecular models can be a meticulous process—even more so when working with nanostructures like carbon nanotubes (CNTs). Whether you’re designing nanoscale sensors, exploring molecular transport systems, or preparing systems for simulation, setting up your model quickly and accurately matters.…

Animating molecular models can often feel like trying to get a group of cats to dance in formation. You know the perfect conformational shift, the right torsion, the intended final position — but getting from frame A to frame B…

Editing molecular structures can sometimes feel frustrating. You move an atom slightly, and suddenly your bond network collapses. Or maybe you’re trying to form a new bond manually but are blocked by invisible forces. These disruptions are often caused by…