Animations are a powerful way to communicate complex molecular mechanisms, transitions, or states. But if you’ve ever struggled to control when specific parts of your molecular model appear in a presentation or animation — you’re not alone. Molecular modelers often…

Before diving into simulations, molecular modelers often face an all-too-familiar problem: starting with a messy structure. Whether importing from experimental data like NMR or public databases, your molecule might contain steric clashes, unrelaxed bond lengths, or awkward conformations. Running a…

Many researchers in academia and industry face the same challenge: powerful new molecular modeling tools exist, but installing them on shared or restricted systems often requires admin privileges. If you’ve ever spent days waiting for IT approvals just to try…

One of the most time-consuming challenges in molecular modeling is not computational—it’s communicational. You’ve built a molecular model or run a simulation, and now you want to present it in an engaging, clear way. Images can only do so much,…

Handling large molecular systems often means dealing with hundreds or even thousands of individual structural components—molecules, residues, atoms, and sometimes metadata or scripts. Keeping track of them all while maintaining focus on your modeling goal can quickly become overwhelming. This…

Molecular dynamics (MD) simulations can provide powerful insights into biomolecular behavior at atomic resolution. But running a successful production MD simulation often comes with hurdles: wrong input paths, mismatched parameters, or just extra time spent redoing steps that could have…

Running molecular dynamics (MD) simulations can be time-consuming, particularly when dealing with multiple molecular conformations or systems. For modelers working with repeated simulations, e.g. for different protein structures or multiple poses of a ligand, having to prepare and simulate each…

If you’ve ever worked with multiple protein structures from the Protein Data Bank (PDB), you’ve probably experienced the repetitive – and tedious – process of cleaning them: stripped waters, removed alternate locations, deleted ligands, added missing hydrogens… the list goes…

When setting up molecular dynamics simulations in GROMACS, it’s often useful—if not essential—to define specific groups of atoms for analysis and specialized operations (e.g., as pull groups or monitoring specific domains). These are known as index groups. While GROMACS can…