Working with large and complex molecular systems can often feel overwhelming, especially when you’re trying to isolate a specific part of your model—ligands, active sites, or particular side chains—for editing, analysis, or visualization. If you’ve ever found yourself switching endlessly…

When presenting molecular systems to colleagues or students, clarity matters. You want to walk them through a complex structure without clutter, and focus their attention on specific regions. But abruptly hiding parts of a structure can be visually jarring—especially in…

Anyone who uses GROMACS for molecular dynamics simulations knows that managing .mdp files can be time-consuming. These files control the behavior of your simulation, but editing them manually every time you switch between minimization, equilibration, and production phases is error-prone…

When working with protein conformational changes, it’s often necessary not only to generate realistic transitions between structures, but also to save and share these transitions for visualization, analysis, or subsequent simulation. If you’re using SAMSON’s ARAP Interpolator to create smooth…

For molecular modelers, a common challenge is to make quick, interactive changes to a molecular system while a simulation is running—without having to restart the setup process from scratch. In SAMSON, the molecular design platform, this challenge is addressed directly…

Protein structure alignment is a crucial step in molecular modeling, comparative analysis, and drug design. Typically, researchers align entire protein structures to assess similarity, calculate RMSD, or map functional residues. But what if your question is only about a small…

When preparing a coarse-grained (CG) molecular system for simulation, one often encounters a subtle but important issue: solvent placement. If not handled correctly, solvation can result in overlapping CG beads, leading to instability during energy minimization or early MD phases.…

Many molecular modelers—especially students and researchers in institutional environments—face a recurring and frustrating challenge: installing advanced software tools on machines where they don’t have administrative privileges. If you’ve ever been excited to try a new modeling platform, only to be…