As molecular modeling projects grow in complexity, manually duplicating and arranging molecular structures can quickly become tedious. Whether you’re assembling a nanotube from scratch or building repeating motifs in materials science or biomolecular models, the goal is the same: replicate…

When modeling molecular systems, understanding how a molecule transitions from one conformation to another can be crucial. These transition paths often characterize reaction mechanisms, ligand unbinding, or conformational changes. However, extracting precise transition information can be computationally expensive and time-consuming,…

Preparing ligands for docking can sometimes feel like a guessing game: are all hydrogen atoms present? Are rotatable bonds under control? Is the molecule properly minimized? If you’ve found yourself spending more time troubleshooting input data than analyzing results, you’re…

Generating initial conformations for umbrella sampling can be time-consuming, especially for researchers who already have a simulation trajectory and want to reuse it efficiently. If you’re using SAMSON’s GROMACS Wizard, there’s a streamlined and visual way to set this up…

Setting up a molecular mechanics simulation can feel like preparing for a journey with no map—especially when working with customizable force fields like the Universal Force Field (UFF). If you’ve ever hesitated because you weren’t sure how to initialize UFF…

One of the surprisingly common pains molecular modelers face is interpolating the motion between two conformational states of a macromolecular complex when those structures differ in the number of atoms or residues. Even small differences can impede trajectory generation, especially…

Running a molecular dynamics (MD) simulation is a critical step in exploring the dynamic behavior of molecular systems like proteins, membranes, or drug candidates. But once the simulation ends, the next challenge can feel just as important — making sense…

For many molecular modelers using GROMACS, customizing simulations often means diving into .mdp files and adjusting text-based parameters manually. While this gives flexibility, it can also be error-prone and lacks visual guidance. What if you could tweak your simulation settings…

When creating molecular animations, there’s often a fine balance between aesthetic fluidity and scientific clarity. A small but recurring challenge arises when a researcher wants to zoom into a particular region of a molecular system without shifting the overall perspective…