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Molecular modelers often face the challenge of evaluating precise distances, angles, and torsions in complex molecular structures. This is crucial for tasks like analyzing interactions, fine-tuning structures, or assessing spatial configurations. If you’ve ever wished for a simple yet powerful…

Molecular dynamics (MD) simulations are an essential tool for molecular modelers, providing valuable insights into the behavior of systems at the atomic level. However, setting up a production MD simulation can be challenging, especially when selecting the right inputs and…

Understanding viral proteins and their mechanisms is critical for researchers, especially molecular modelers, working on advancing virology, immunology, and drug design. One of the most intriguing examples is the SARS-CoV-2 spike protein, which plays a crucial role in the virus’s…

Sometimes, working with the latest version of a software isn’t always ideal. Whether it’s for compatibility reasons, specific features, or personal preference, molecular modelers may find themselves needing to work with an older version of the software. Here’s how SAMSON…

Imagine crafting a molecular animation where the camera elegantly orbits around a protein structure or seamlessly zooms into an active site to create a compelling story. Visual narratives are crucial to explaining complex molecular processes, and camera animations in SAMSON…

When running molecular dynamics simulations with GROMACS, precise control over groups of atoms can play a pivotal role in analyses and custom workflows. While GROMACS automatically generates standard index groups (e.g., protein, solvent, ions), did you know you can define…

Center-of-mass (COM) pulling is an essential technique in molecular modeling, especially for simulating molecular interactions, exploring conformational changes, or setting up umbrella sampling studies to calculate free energy profiles. However, getting started with COM pulling simulations can be daunting due…