When preparing a molecular dynamics simulation, one often-overlooked but important decision is the shape of the unit cell used for applying periodic boundary conditions. This decision can impact both the accuracy and performance of your simulation. If you’ve ever wondered…

Deciding on parameters for a production molecular dynamics (MD) simulation can be one of the most deceptively time-consuming tasks in computational molecular modeling. The settings you choose—such as the number of steps, the time step size, and coupling constants—can significantly…

Many molecular modelers rely on GROMACS for running molecular dynamics simulations. It’s fast, robust, and widely used. However, there’s one issue that pops up often: how to use your specific version of GROMACS from within another platform or software like…

One of the most frequent challenges in molecular modeling is dealing with incompatible file formats. Whether you’re preparing a system for simulation, analyzing results, or sharing data with collaborators, you’ve likely faced the annoyance of having to convert files or…

For molecular modelers and structural biologists working with complex molecular systems, presenting molecules in a clear and digestible way can be a real challenge—especially when you’re trying to guide an audience through a process, a mechanism, or a sequence of…

If you’re modeling molecular systems with multiple molecules, you’ve probably encountered this issue: you want to fine-tune a single molecule or part of it without affecting the rest of your system. Maybe you’re adjusting a ligand conformation in a protein-ligand…

If you’ve ever created molecular presentations or movies, you’ve likely encountered this common issue: your molecules look exactly right in one frame and completely off in the next. This is especially true when animations are missing camera transitions or your…

If you’ve ever handled multiple PDB files, you know the pain of preparing them one at a time before a molecular modeling workflow. Manually opening each structure, checking for alternate locations, removing waters or ions, and adding hydrogens can easily…

One frequent challenge in molecular modeling is effectively visualizing and communicating the motions of molecules. Whether you’re studying a ligand as it exits a binding site or analyzing a protein conformational pathway, being able to show a trajectory in reverse…