Umbrella Sampling is a powerful molecular dynamics technique to study the free energy landscape of complex systems. However, setting up the initial configurations for such simulations can be daunting. In this blog post, we’ll explore how the GROMACS Wizard in…

For molecular modelers, navigating complex macromolecular structures and working with multiple chains can be daunting. Have you ever spent too much time trying to focus on a specific sequence or accurately link your selections across views? SAMSON addresses this challenge…

One of the key challenges for molecular modelers is analyzing energy data efficiently to make sense of their simulations. Whether comparing potential and kinetic energies, or tracking energy along a molecular path or trajectory, accurate energy analysis can provide valuable…

In molecular modeling, the ability to explore complex protein motions is critical for understanding biological processes. One such challenge is analyzing the motion of the SARS-CoV-2 spike protein, which is central to how the virus binds and gains entry into…

When performing molecular dynamics simulations with pulling, defining precise index groups for targeted molecules or chains is a critical step. However, molecular modelers often struggle with creating these groups efficiently. This blog post walks you through how to create custom…

Molecular modeling often involves dealing with complex systems with numerous nodes, from atoms to residues and entire molecular structures. Navigating and managing these elements can be time-consuming, especially when repeatedly targeting specific selections for analysis or visualization. Enter Quick Groups,…

When exploring ligand unbinding pathways during molecular modeling projects, it’s crucial to have tools that efficiently export and visualize results. Understanding how to manage your pathway results in SAMSON’s Ligand Path Finder app can help molecular modelers turn raw calculations…

If you’ve ever needed to export ligand trajectories for free energy calculations or reaction coordinate analysis, you know how time-consuming it can be to prepare the data. With SAMSON’s Export Along Paths extension, this process becomes significantly easier, helping you…