If you’ve ever needed to visually represent how molecules come together during docking in your presentations or simulations, SAMSON’s Dock animation offers a smooth and intuitive way to make that happen. One common pain point for molecular modelers is the…

When studying ligand migration or unbinding processes in proteins, it’s often essential to extract and analyze the precise atomic trajectories along the computed paths. Whether you’re feeding the data into further simulations, building visualizations, or compiling a presentation, being able…

One of the most common pain points for molecular modelers performing protein-protein docking is the time it takes to get meaningful results. Exhaustive searches across all possible orientations are computationally intensive, especially when docking larger biomolecules. If you’ve found yourself…

If you’ve ever waited too long for a molecular geometry to optimize, you’re not alone. A common bottleneck in molecular modeling is the slow convergence of standard algorithms like Steepest Descent — especially when dealing with large systems or complex…

One frequent challenge in molecular modeling is understanding how a protein transitions from one structure to another. Traditional molecular dynamics simulations can take a lot of time and computational power—even for visualizing a simple pathway between two known conformations. If…

Running production molecular dynamics (MD) simulations can very quickly turn into a juggling act for molecular modelers: multiple files, simulation logs, and trajectories all need to be carefully tracked. If you’re running several simulations — maybe testing different parameters, different…

When you’re preparing a molecular presentation—whether for a class, a paper, or a conference—one of the biggest challenges is guiding your audience’s attention. Just like in film, controlling the camera is what allows you to tell a coherent and visually…

Water is everywhere in biological systems, but when it comes to preparing a protein structure for simulations in GROMACS, not all water molecules need to stay. In fact, a common challenge faced by molecular modelers is identifying and removing only…

When simulating molecular systems, researchers often need to model multiple copies—or replicas—of the same protein. This is especially relevant for studying concentration effects, protein aggregation, or large-scale interactions. But generating coarse-grained (CG) models for these replicas can become a tedious…