Author: OneAngstrom

One of the common challenges for molecular modelers performing umbrella sampling is defining the reaction coordinate in a reproducible and visual way. Whether you’re studying ligand unbinding, protein–protein interactions, or mechanical unfolding, the accuracy of your free energy profile depends…

If you’ve spent time setting up molecular systems in a modeling environment, you know how tedious it can be to select atoms, residues, or chains — especially when you’re working with large biomolecular complexes. Writing specific selection scripts or navigating…

Getting Umbrella Sampling right often starts with one frustrating step: selecting meaningful initial conformations. Should you extract frames from a trajectory? Or start from a pathway of your own? How many conformations are enough? Picking them manually, or writing custom…

Understanding the structural transitions of viral proteins is key in drug discovery and vaccine development. One of the most critical mechanisms in SARS-CoV-2 infection is the conformational change of the spike (S) protein from a closed state to an open,…

Building polymers in molecular modeling often starts off fine—until you hit the roadblock of customization. Maybe you’re designing a novel material, exploring backbone flexibility, or preparing conjugated architectures. But when it’s time to define your own monomers, many existing tools…

Precise orientation of molecular models is essential in many modeling workflows, from preparing simulations and comparing molecular structures to generating reproducible visualizations. Yet, achieving consistent alignment can be tedious, especially when done manually. If you’re working with molecular structures, meshes,…

If you’ve ever struggled to distinguish between important parts of a molecular model due to color confusion or visual overload, you’re not alone. A common pain point in molecular modeling is using color schemes that are either too harsh, too…

When running molecular simulations with GROMACS, organizing parts of your system into logical groups can make a huge difference in analysis and setup—especially if you need to define regions of interest like specific residues or structural motifs. In GROMACS terminology,…