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…

One of the key challenges in molecular modeling and drug design is efficiently exploring structural variations of a molecule to identify modifications that improve desired properties. This is often an iterative and time-consuming process, requiring trial and error to find…

Running molecular dynamics (MD) simulations can be computationally intensive, especially when dealing with large systems. For many researchers, these heavy computational requirements can slow down project workflows and strain local hardware. What if there was a way to offload these…