One of the most common challenges in molecular modeling is reviewing and presenting dynamic changes across different conformations or simulations. Whether you’re studying protein folding, ligand docking, or large-scale molecular motions, being able to visualize changes smoothly over time is…

Have you ever struggled to share the results of your molecular simulations or structural analyses in a way that truly captures the complexity of what you’re studying? Static images can be useful, but they often fall short when it comes…

One common challenge in molecular design is quickly generating diverse analogs of a lead compound to test for biological activity, stability, or solubility—without having to draw every single structure manually. This is especially important in lead optimization phases, where chemists…

When setting up center-of-mass (COM) pulling simulations in GROMACS using SAMSON’s GROMACS Wizard, one key step that often raises questions is how to properly define and use custom index groups. This step is essential if you want to pull specific…

Molecular simulations often require running the same protocol for multiple initial states. Whether you’re performing Umbrella Sampling, exploring conformational variability, or evaluating system responses, you likely need to simulate not just one, but many conformations of the same molecule. This…

When modeling molecular pathways—like a ligand unbinding from a protein pocket—researchers often face a simple but frustrating problem: how to export atomic coordinates along a simulated path, but only for the atoms of interest (e.g. the ligand or a specific…