Author: OneAngstrom

Anyone who has worked with GROMACS has likely run into this issue: you want to analyze a specific part of your system—maybe all alpha helices, or a binding pocket—but the default index groups just don’t cut it. Manually configuring these…

Designing new molecules often involves tweaking known structures – replacing parts of a molecule to generate analogues for screening. This process can be both time-consuming and error-prone when done manually, especially at scale. If you’re working in drug design, materials…

Whether you’re simulating a protein-ligand complex or a large membrane system, defining the right parameters for your molecular dynamics (MD) simulations can be tricky. Even experienced users of GROMACS sometimes overlook critical details when transitioning from equilibration to production MD.…

Preparing systems with multiple protein replicas is a common need in coarse-grained molecular modeling, especially when studying self-assembly or concentration effects. Yet, what seems like a simple task—duplicating a single protein structure several times—can quickly turn into a frustrating experience…

When creating molecular animations, clarity is everything. Whether you’re illustrating mechanisms of action, molecular interactions, or structural rearrangements, guiding your audience’s focus without overloading the scene is a challenge. One effective way to enhance focus is by hiding parts of…

For many researchers and students working in universities, biotech companies, or public labs, installing software without administrator rights can be surprisingly difficult. IT policies, locked systems, and resource approval cycles often get in the way—preventing scientists from quickly testing or…

Visualizing molecular transformations can be challenging, especially when you want to guide your audience’s attention through a clear and digestible path. One common request from molecular modelers and presenters is the ability to create clean transitions between different components of…

One of the challenges many molecular modelers face when analyzing the flexibility and dynamics of biomolecules is keeping track of interesting conformations or motion trajectories. Whether you’re preparing a figure for publication, comparing several states of your molecule, or simply…

Adding lipid layers around proteins is a common requirement in molecular modeling, especially for studying membrane proteins and receptor dynamics. But the process often feels unintuitive, involving multiple software tools, scripts, and tedious alignment steps. If you’ve ever struggled to…