Author: OneAngstrom

Working with complex molecular systems often means handling thousands, even millions of atoms, residues, chains, and other entities. For molecular modelers, selecting specific parts of a model—like all oxygens within a certain range from a binding site—is a common but…

One of the recurring challenges when working with complex molecular systems is the precise editing of atomic or structural properties without disrupting the relationships between nodes. For example, what happens if you want to change the position of a group…

One of the subtle yet critical steps when setting up molecular dynamics (MD) simulations with coarse-grained (CG) models is ion addition. If not handled properly, the system can become unbalanced or lead to non-physical behavior during simulation. Fortunately, the GROMACS…

Simulation parameters can make or break the success of a molecular dynamics (MD) run. Whether you’re doing energy minimization or running production simulations, getting those .mdp settings just right is essential. But if you’ve ever spent time tweaking GROMACS parameter…

One of the most common frustrations molecular modelers face is lack of control over how simulation tools interpret chemical structures. Automatically detected atom types and bond orders are often sufficient, but there are many cases—organometallic systems, delocalized bonding, non-standard valence—where…

When preparing molecular animations, clarity of movement is key—especially if you want to communicate what is happening in a dynamic system effectively. One common challenge for molecular modelers is how to move the camera vertically in a scene while keeping…

For many molecular modelers, a frequent source of frustration is getting that one fragment to align just right. Whether assembling a ligand into a binding pocket or fusing building blocks into nanostructures, orientation matters. A slight misalignment can mean hours…

Visualizing molecular motion is one of the most compelling ways to understand complex structural dynamics. Whether you’re working on protein flexibility, ligand binding, or simply preparing an educational presentation, showing how a structure might move can strengthen your message. But…