Author: OneAngstrom

One of the subtle pain points in molecular modeling is choosing effective colors that communicate your data clearly. Whether you’re differentiating chains in a protein, visualizing atom types, or building figures for publications, poor color choices can easily confuse viewers…

When running molecular dynamics simulations—especially in a coarse-grained (CG) setup using the MARTINI force field—preparation is key. One often overlooked but crucial step is ensuring your system is properly neutralized and has the right salt concentration. This blog post walks…

Molecular modelers often spend significant time preparing animations to showcase structural motions, interactions, or simply to produce high-quality visuals for sharing with collaborators or in presentations. But once the structure is prepared, how do you generate smooth, professional-looking camera movements…

Molecular modelers frequently need to analyze how ligands move along defined pathways — whether for reaction coordinate studies, intermediate conformation extraction, or free energy calculations. But what if you’re only interested in the ligand, not the whole system? Exporting entire…

Creating compelling molecular animations often requires precise control over the visibility of elements in your scene. Whether you’re showcasing a binding site, highlighting a conformational change, or simply guiding viewers through a molecular mechanism, what you choose to hide—and when—is…

When preparing molecular presentations or animations, clarity and focus are everything. Whether you’re showcasing a binding site for clarity, highlighting a ligand interaction, or trying to subtly direct the viewer’s attention, camera movements go a long way. But have you…

When preparing biomolecular systems for molecular dynamics simulations with GROMACS, one common but confusing step is deciding what to do with crystal water molecules. Should all crystallographic water be deleted? What if some are essential to the protein’s function? This…

Staring at brightly lit interfaces late at night while working on detailed molecular structures can be tiring and distracting. For molecular modelers who spend hours analyzing complex geometries, renderings, and atomistic simulations, eye strain caused by bright themes is a…