When working with molecular systems in GROMACS, detailed analysis and advanced simulation setups such as umbrella sampling or pulling simulations often require specific selections of atoms or residues. These selections are managed using index groups. GROMACS automatically generates standard index…

Anyone who has worked with multiple protein structures knows the challenge: each file needs cleanup before starting a molecular dynamics simulation, docking calculation, or structural analysis. Removing water, handling alternate locations, fixing missing hydrogens—it’s the sort of repetitive task that…

In molecular dynamics simulations, the Energy Minimization (EM) step helps relieve atomic clashes and brings the system to a physically realistic starting point. It’s often one of the first steps after preparing your system, but sometimes it just won’t converge—and…

Molecular simulations often involve tracking complex atomic rearrangements: docking events, folding pathways, or drug interactions. But replaying those subtle moves isn’t always straightforward. If you’ve ever needed a clean, visual representation of how atoms moved throughout a simulation for presentations…

Molecular modelers often face a recurrent frustration when studying large biomolecular structures: the lack of dynamic, visual insight into conformational transitions. This is particularly true for complex glycoproteins like the SARS-CoV-2 spike protein, which plays a central role in viral…

When preparing a molecular animation—for a presentation, a class, or a social media post—clarity is everything. Visual clutter, overlapping elements, or sudden disappearances can distract your audience and cloud your key message. This is especially true when you want to…

If you’ve ever tried to work with molecular structures from a variety of sources, you’ve likely faced the challenge of incompatible file formats. Maybe you received data from a collaborator in a format your tool doesn’t recognize. Or perhaps you…

Molecular modelers often face challenges when presenting their research effectively—especially when trying to integrate molecular scenes with presentation elements like background slides or contextual imagery. In team meetings, research talks, or teaching, conveying your message clearly and attractively matters. This…

When performing molecular dynamics simulations involving center-of-mass (COM) pulling, failing to correctly define the simulation box can lead to artifacts—especially when periodic boundary conditions come into play. One common challenge molecular modelers face is ensuring that enough space exists in…