When modeling the flexibility of biomolecules, it’s common to analyze and generate alternative conformations that represent plausible intermediate or functional states. However, there’s often a challenge that arises: once you’ve arrived at an interesting conformation or motion through computational tools,…

One common challenge molecular modelers face when performing umbrella sampling simulations is the post-processing step: extracting the Potential of Mean Force (PMF) from a set of umbrella windows. Setting up the right environment, finding coordinated inputs from multiple simulations, and…

When studying molecular interactions, especially those involving binding or unbinding events, researchers often need access to atomic coordinates along well-defined paths. These trajectories are useful for reaction coordinate analysis, free energy calculations, or simply visualizing how a ligand travels through…

Crystalline materials in the real world often deviate from their ideal structures. Imperfections such as vacancies, substitutions, or interstitials—collectively known as defects—can dramatically influence material properties like conductivity, strength, and optical behavior. Simulating these defects realistically is essential for researchers…

In molecular modeling and simulations, visualizations are essential for storytelling. Whether you’re preparing a conference talk, sharing a molecular mechanism on social media, or teaching students about molecular interactions, how you present your model can affect understanding and engagement. One…

Anyone working with molecular dynamics (MD) simulations knows the pain: you’re ready to analyze some subtle motion or apply restraints during your GROMACS run, and the default index groups just won’t cut it. You need something specific — a pocket,…