When preparing a molecular system for simulation, especially with tools like GROMACS, one of the early and often overlooked steps is deciding which crystal waters to keep and which to remove. This may seem straightforward at first—just remove all water…

When creating animations of molecular systems, the camera view can sometimes unexpectedly shift between frames. This often happens when working on long simulation trajectories or assembling scenes over time, leading to moments of disorientation or inconsistent visual storytelling. Fortunately, the…

Whether you’re building a homology model, refining a predicted structure, or preparing a system for simulation, strained backbone conformations can introduce problems. Outliers in φ (phi) and ψ (psi) backbone dihedral angles may go unnoticed in a 3D viewer, but…

Molecular modelers often face a recurring challenge: they have powerful stand-alone tools or custom scripts that work well in isolation, but integrating them into a larger working environment with visualization, simulation, and interactive editing can be difficult and time-consuming. If…

When working with complex protein-ligand systems in solution, one of the biggest bottlenecks in using Nuclear Magnetic Resonance (NMR) data—especially for integrative modeling—is the time it can take for structure prediction tools to evaluate all possible methyl group combinations. If…

Visual clarity is a recurring challenge in molecular modeling. When working with complex structures—particularly in 3D—being able to intuitively grasp spatial relationships between atoms and molecules can significantly improve understanding and communication. Whether you’re preparing publications, creating teaching materials, or…

When preparing a biomolecular system for simulations in GROMACS, one common step is to remove water molecules from the structure. However, indiscriminately deleting all water can lead to the removal of functionally important or tightly bound waters, especially those located…