When setting up molecular dynamics simulations of membrane proteins, one of the most repetitive and error-prone steps is placing a lipid layer or bilayer around the protein. Aligning the protein, choosing the right lipid orientation, adjusting the box dimensions, and…

Creating immersive animations in molecular modeling isn’t just about rotating a protein or zooming into an organometallic complex. The real challenge often lies in guiding the viewer’s eye smoothly, helping them focus on what matters, and making the experience feel…

When creating animations of molecular processes, clarity and timing can make all the difference. Whether you’re showing molecular assembly, drug docking, or simply highlighting part of a structure, there’s often a need to make specific groups of atoms appear progressively…

Anyone running molecular dynamics simulations with GROMACS has likely come across the challenge of managing and reusing .mdp files. These parameter files are essential, but editing them manually can be error-prone. More often than not, researchers keep a cluttered folder…

For many molecular modelers, setting up and running molecular dynamics simulations with GROMACS can be a balancing act between simulation precision and computing power. While local machines often serve well for small systems or short simulations, more complex or longer…

When constructing complex molecular systems, one common challenge modelers face is positioning fragments exactly where they should go. Whether you’re combining rings, functional groups, or biomolecular motifs, ensuring correct orientation can make or break your structure. Misplaced fragments can lead…

One of the most common challenges in molecular modeling is making sense of complex molecular systems. Beyond raw data like atom coordinates, researchers need intuitive visual representations to explore, analyze, and communicate their findings effectively. This is where visual models…

Interactive energy minimization is one of the most common steps in preparing molecular structures for modeling, especially when repairing imported geometries or refining parts of a system. However, many molecular modelers face the challenge of needing to minimize only a…