When exploring large biomolecular structures in molecular modeling, one of the frequent needs is identifying specific residues by their chemical properties. Whether refining a force field, preparing an input file, or designing a mutation experiment, knowing exactly where the positively…
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…
For computational chemists and molecular modelers, screening structural groups based on charge is often key to understanding reactivity, electrostatics, or guiding docking simulations. But quickly identifying molecular groups based on total partial charge in a large system can be cumbersome…
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…
Anyone working in molecular modeling has faced this at least once: after spending hours crafting a molecular structure, either to simulate a reaction, visualize an experimental result, or design a new molecule, you suddenly need to export it—to quickly share…
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…
One common frustration for molecular modelers using SAMSON is discovering that a SAMSON Extension fails to load at startup. This usually happens after installing a new Extension or updating the SAMSON platform. Fortunately, there’s a straightforward explanation for this behavior,…
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…
