Many molecular modelers run into the same problem when trying to refine a local geometry: they want to minimize just part of a molecule without affecting everything else. Say you’ve modified a side chain, added a ligand, or just built…

When preparing molecular animations or visual protocols in SAMSON, one common frustration is dealing with unintended camera movements that disrupt the flow of a presentation. Many users don’t realize that the view of their molecular system may shift unexpectedly if…

One common struggle for molecular modelers is turning complex molecular data into clear, insightful visualization. Whether you’re analyzing a protein’s folding, looking at an electron density map, or comparing molecular surfaces, effective visual representation is often the first step toward…

For molecular modelers dealing with polymers, flexibility is key. Whether you’re exploring polymers for materials science or designing synthetic biopolymers, you often start from specific molecular fragments or building blocks. But turning those fragments into reusable, structured monomer units can…

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…