Author: OneAngstrom

Molecular modelers working with carbon nanotubes (CNTs) often need to generate structures quickly to test ideas, verify hypotheses, or initiate simulations. However, many tools place barriers such as command-line syntax, abstract parameters, or pre-baked models that don’t reflect exact needs.…

One common challenge for molecular modelers is performing large-scale or lengthy GROMACS simulations without overloading their local machines. Interactive work becomes sluggish, fans spin up, and background simulations may suddenly halt if the system goes idle or reboots. What if…

One of the most overlooked yet crucial steps in preparing coarse-grained molecular dynamics (MD) simulations is solvent and ion setup. If coarse-grained (CG) models are incorrectly solvated or ionized, simulations often produce unrealistic results—or fail entirely. This blog post focuses…

Molecular modeling can often feel repetitive when tasks like structure modification, selection, transformation, or even simple visualization require many manual steps. If you’ve ever wished there was a faster, more intuitive way to interact with your models—perhaps even generate nanotubes…

Managing complex molecular models—especially those involving large biomolecular systems, multiple ligands, or reference structures—can become overwhelming. Most molecular modelers have faced the frustration of cluttered data views, accidentally hiding key elements, or applying actions to unintended parts of a model.…

If you’ve ever docked a ligand library and received unimpressive binding poses, misleading scores, or just downright strange conformations, there’s a high chance the source was not AutoDock Vina itself—but the ligands you fed into it. One of the most…

If you’ve designed DNA nanostructures in Cadnano, there’s a good chance you’ve hit a wall when trying to bring those designs to life in 3D with more flexibility and detail. Whether you’re preparing for a simulation, looking to merge multiple…

When working on complex molecular modeling tasks, mistakes are inevitable. You might accidentally delete a structure, misplace a functional group, or alter a configuration that took hours to prepare. These small mishaps can significantly impact your productivity—unless you have a…

For molecular modelers, one recurring task is converting SMILES strings into full 3D molecular geometries. Whether you’re analyzing ligand conformations or preparing a virtual screening campaign, the ability to quickly visualize realistic 3D models from SMILES can save hours of…