Author: OneAngstrom

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…

When working with molecular models, especially across multiple projects or complex molecular systems, keeping your workspace clean and organized can be a real challenge. Structures, scripts, data files, different conformations—everything can pile up quickly. If you’ve ever struggled with finding…

Communicating complex molecular processes or simulation results often involves building animated presentations. But often, the focus is exclusively on molecular geometry and motion, leaving the background of your presentation static or blank. This can limit clarity when walking an audience…

When building animations of molecular systems, clarity is key. Scientists often need to guide the viewer’s attention by revealing or removing parts of a complex molecular structure at the right moment. But creating these effects manually—especially when working with large…

Before you hit the “Run” button on a molecular dynamics simulation, one seemingly small but critical decision can save you hours of confusion: selecting the correct input structure. If you’re using GROMACS Wizard in SAMSON for an NVT Equilibration run,…

When viewing a molecular system, a list of coordinates or a ball-and-stick representation can get you only so far. Molecular modelers often need to see what matters—secondary structures, surfaces, fields, or density isosurfaces—to understand interactions, identify regions of interest, or…