Author: OneAngstrom

Molecular modelers often face a recurring challenge when studying conformational changes in large biomolecular systems: how to generate a realistic trajectory between two known structural states. This issue becomes more complicated when the two states differ significantly, as is the…

Setting up GROMACS for molecular dynamics simulations can be a real roadblock for many researchers. Between compiling the package, ensuring all dependencies are correctly met, and navigating version compatibility issues, it’s no surprise that time is often spent troubleshooting before…

Molecular dynamics simulations are rarely one-size-fits-all. If you’ve ever needed to tweak temperature coupling, adjust time steps, or fine-tune constraints for your system, you’re not alone. Default settings are great for getting started, but real science often calls for customization.…

One of the more time-consuming challenges in molecular modeling is having to constantly switch between different tools or manually write scripts to bridge gaps between specific needs and the capabilities of existing software. Whether you’re trying to customize a simulation…

When preparing a molecular dynamics simulation involving pulling—such as center-of-mass (COM) pulling—one of the most overlooked yet critical steps is correctly defining the simulation box size. A common pitfall for modelers is encountering artifacts due to improper box dimensions, especially…

One of the most common questions molecular modelers have when setting up docking experiments is: “Where should I define the search space?” Whether you’re targeting a known binding pocket or screening broadly across the protein, defining the search domain correctly…

Presenting complex molecular models can be a challenge when important parts of the structure overlap or obscure one another. Whether you’re preparing a presentation, recording a molecular animation, or just trying to better understand your system, being able to temporarily…

When preparing molecular animations for presentations or scientific communication, molecular modelers often face a recurring challenge: how to present the structure dynamically without altering its real position? Sometimes, rotating or moving the molecule can be misleading or distracting—especially when showing…

Going from a list of SMILES strings to functional 3D molecular structures can still feel like a chore, especially when you need to process multiple molecules quickly and visualize them in appropriate software. If you’re working in drug discovery, molecular…

Accurately comparing proteins is a cornerstone of molecular modeling, whether you’re examining point mutations, comparing homologs across species, or preparing a structure for homology modeling. But when working with multi-chain proteins or oligomeric complexes, sequence alignment at the chain level…