Molecular modelers and researchers working to understand the SARS-CoV-2 virus often encounter a specific challenge: analyzing and simulating the complex opening motion of the virus’s spike proteins. This motion is crucial for studying how the virus interacts with human cells,…

For molecular modelers, efficiently exporting atomic trajectories along predefined paths can greatly enhance workflows such as reaction coordinate studies, free energy calculations, and ligand pathway analysis. This guide focuses on how SAMSON’s Export Along Paths extension simplifies this process, saving…

For molecular modelers and researchers, presenting complex molecular structures in an engaging and insightful way is a crucial part of their work. When it comes to creating impactful visualizations, animations like the Orbit Camera in SAMSON can make a significant…

Preparing molecular systems for simulation can often feel like an odyssey, particularly when working with complex proteins or custom setups. Issues such as alternate atom locations, unnecessary waters, unwanted ligands, or extraneous ions can cause confusion and errors down the…

For molecular modelers, handling computationally heavy simulations can be challenging, especially when local hardware struggles with system size or complexity. The GROMACS Wizard in SAMSON provides an elegant solution: running simulations in the Cloud. Let’s dive into how you can…

If you’ve ever struggled to clearly demonstrate the structural composition of a molecular system, the Disassemble animation in SAMSON could be the streamlined solution you need. Visualizing how molecular models split into their individual components can provide deeper insight into…

For molecular modelers, simulation accuracy and reproducibility are cornerstones of success. However, these principles present unique challenges when using pre-packaged molecular dynamics software. One such challenge? Ensuring the version of GROMACS matches your unique computational requirements or reproducibility standards. The…