Author: OneAngstrom

Working on complex molecular systems often means jumping back and forth between different parts of a structure—ligands, receptors, water molecules, or specific chains. Manually reselecting these parts again and again is time-consuming and can break your flow. That’s where Quick…

In computational molecular modeling, trial and error is often part of the discovery process. Whether you’re building a structural model, setting up a simulation, or analyzing a complex interaction, it’s common to make adjustments—some of which you’d rather undo. But…

Preparing a coarse-grained system for molecular dynamics (MD) simulations can be surprisingly tricky — especially when it comes to solvation. When you’re using MARTINI v.3.0.0 force field models in SAMSON’s GROMACS Wizard, one of the most frustrating issues you might…

Molecular modelers and educators often face the challenge of communicating dynamic processes effectively—like binding events, conformational changes, or molecule appearances during reactions. In molecular animation, when and how certain elements appear or disappear can make a big difference in how…

One of the common challenges in molecular modeling—especially when working with drug discovery or protein-ligand interaction—is understanding how a ligand moves as it unbinds from a protein. Visualizing this motion not only helps interpret simulation results but also improves communication…

Have you ever needed to clearly illustrate how a ligand detaches from a receptor in a molecular complex during your presentations or simulations? Whether you’re preparing educational materials, creating a scientific demo, or simply visualizing transitions in molecular assemblies, demonstrating…

One of the most important steps in running a successful Umbrella Sampling workflow is the definition of the reaction coordinate. This choice will directly impact the relevance and clarity of the computed Potential of Mean Force (PMF) profile. However, selecting…