If you’ve ever opened a PDB file and been disappointed to find only part of the structure—just one chain or a fragment of a protein complex—you’re not alone. Many researchers assume PDB files always include the full biological assembly. Instead,…

Designing carbon nanotubes or other tube-like molecular structures has traditionally required a combination of scripting skills, structural chemistry knowledge, and often repetitive modeling steps. If you’re working in nanotechnology, materials science, or molecular modeling, you’ve likely spent time trying to…

When working with complex molecular models, precise alignment becomes critical—especially when comparing structures, preparing input files for simulations, or creating meaningful visualizations. Misaligned structures can lead to errors in analysis, inefficient setups for simulations, and ambiguous visual outputs. Fortunately, SAMSON…

When setting up a GROMACS simulation, you may find yourself needing to analyze a specific portion of a molecular system repeatedly — certain backbone atoms, a ligand, or, for instance, residues forming alpha-helices. In standard GROMACS workflows, this often requires manually…

In molecular modeling, clarity is key—especially when communicating complex structures to a broader audience. Whether you’re preparing a presentation, making educational content, or exploring your designed molecules, visualizing molecular components separately can provide immediate insight into structure-function relationships. This is…

Communicating complex molecular mechanisms often requires more than static images. Whether you’re creating molecular tutorials, preparing research presentations, or simply trying to make your findings clearer to non-specialists, animation can make a real difference. But not all animations are about…

One common obstacle faced by molecular modelers when working with molecular dynamics (MD) simulations is managing input files correctly between simulation stages. If you’ve ever had to rerun an NPT equilibration in GROMACS just because you didn’t set the right…

For molecular modelers analyzing protein conformational changes, it’s often not enough to just visualize start and end structures. Understanding the atomic-level movements along the transition path is key to gaining insights into protein mechanisms, identifying stable regions, and preparing for…

Researchers and developers working in molecular modeling often face a common challenge: how to integrate their own simulation methods, tools, or workflows into their modeling platform. Whether it’s a newly developed algorithm, a custom-built force field, or a connector to…

Understanding how a ligand navigates through a protein tunnel or binding pocket is crucial in molecular modeling. If you’re analyzing ligand unbinding or conformational transitions, it’s often difficult to see the bigger picture of a movement just by playing through…