Author: OneAngstrom

When working with Protein Data Bank (PDB) files, molecular modelers often face a limitation: the structures frequently describe only asymmetric units—just a part of the full biological or crystal assembly. This can make it hard to visualize or simulate the…

If you’re running molecular dynamics simulations or exploring binding/unbinding pathways, you’ve probably encountered this question: where does the system actually go? While we often track individual atoms or align structures, it’s not always easy to get an intuitive grasp of…

One of the recurring bottlenecks for researchers running molecular simulations with GROMACS is managing input files across multiple stages: preparation, energy minimization, equilibration, and production. Errors often arise when selecting outdated or mismatched input paths, especially in multi-step workflows or…

When modeling complex molecular systems, it’s easy to find yourself juggling various tools that manipulate, select, or construct parts of the model. SAMSON streamlines this experience using editors — interactive tools designed to help you edit molecular models efficiently. But…

When preparing molecular animations, it’s often not just about clarity — it’s also about timing. You may want to slow things down at a crucial moment in your molecular presentation to give your audience a chance to absorb what they’re…

When preparing coarse-grained (CG) molecular systems for simulation with GROMACS, one of the crucial—but often overlooked—steps is setting the proper van der Waals distance for solvation. If this value is left unchanged, the solvent might clash with solute beads, leading…

Whether you’re preparing a talk, creating a recorded walkthrough, or simply documenting molecular interactions for a team meeting, visualization plays a key role in helping others understand your work. But what happens when your visuals are cluttered, or worse –…

Colors aren’t just visual flair in molecular modeling—they are crucial tools for understanding. When dealing with complex molecular structures, reaction networks, or simulation results, using clear, distinguishable colors helps avoid confusion and supports better decision-making. In SAMSON, discrete color palettes…