One common challenge in computational molecular design is correctly preparing a protein-ligand system for dynamic simulations. Poor initial setup can lead to unusable results or misleading data, especially when exploring ligand unbinding pathways. In this post, we focus on a…

When working with crystallographic or biological assemblies of proteins, understanding how subunits are arranged is essential. Whether you’re modeling quaternary structures or designing symmetric nanostructures, replicating and visualizing symmetric interfaces can be a key step. But generating all symmetry mates…

For many molecular modelers, setting up coarse-grained (CG) molecular dynamics (MD) systems can be a tedious and error-prone task. Between topology generation, solvation, ion addition, and force field configuration, it’s easy to get stuck in a series of manual steps…

Communicating a molecular mechanism often means going beyond static images. Whether you’re presenting a conformational change, a binding process, or a protein-ligand interaction, being able to illustrate spatial structure clearly is essential. One common challenge? Providing viewers (or yourself) with…

When molecular models become dense or structurally complex, it’s easy to lose track of key regions in your presentation. Whether you’re demonstrating binding interactions, structural differences, or pathway progression, isolating areas of interest can be crucial for communication. The Conceal…

When setting up molecular dynamics (MD) simulations using GROMACS, one decision often overlooked—but critically important—is the choice of the unit cell shape used in periodic boundary conditions (PBCs). The shape of your simulation box directly impacts resource usage and simulation…

If you’ve ever spent time crafting molecular animations to convey a complex process — say, ligand binding or conformational change — you might have noticed that visual clarity is just as important as scientific accuracy. Too many objects on the…

Many molecular researchers experience a common yet frustrating obstacle: installing advanced molecular modeling tools on systems where administrative permissions are limited or completely restricted—especially in academic institutions, shared labs, or virtual environments. If you’ve ever faced such a hurdle, you’ll…