When you are studying large macromolecular systems, one notoriously difficult task is to simulate plausible transitions between two known conformations. Whether you’re investigating protein folding, loop dynamics, or viral mechanisms, modeling intermediate structures between an open and closed state can…

Anyone who has worked with GROMACS knows that defining the right index groups can be a challenge—especially when your system involves complex molecular structures or you’re setting up simulations like center-of-mass (COM) pulling. If you’ve ever found yourself tediously creating…

When creating molecular animations, clarity and visual fluency can make or break the message. Whether you’re showcasing ligand binding, structural transitions, or simply guiding your audience through a complex biological environment, how you move the camera matters. But moving the…

When creating molecular animations, smooth transitions and stable perspectives are crucial. Whether you’re preparing a video for publication, a lecture, or a team presentation, you want your viewers to focus on the molecular systems— not wonder why the camera view…

One of the most common challenges molecular modelers face is managing and sharing complex projects. From structural models and simulation data to custom Python scripts and supporting documents, research often stretches across numerous files and folders. This becomes especially tricky…

When you’re building compelling molecular presentations or setting up reproducible animations for visual analysis, ensuring smooth and consistent camera motion is essential. Vertical movements in particular can be tricky—especially when you want to maintain orientation while transitioning focus between molecular…