Author: OneAngstrom

Molecular modeling often comes with its own set of complexities, particularly when managing and modifying attributes of selected atoms or groups of nodes. Have you ever made adjustments and wished to revert specific values to their default state without undoing…

Molecular modelers often face challenges when trying to create custom nanoscale structures and manipulate atomic models with precision. This task can be particularly time-consuming without the proper tools and workflows. Fortunately, the Simple Script Extension in SAMSON is here to…

Molecular modelers often encounter challenges when attempting to simulate real-world crystals. Among these challenges, accounting for crystal defects—such as atom vacancies—is essential for accurately representing materials. The Crystal Creator Extension in SAMSON offers an intuitive way to explore and model…

For molecular modelers, computational resources often become a bottleneck. Running complex simulations such as molecular dynamics (MD) or equilibrations locally can put immense strain on personal devices, and frequently such systems are too large or time-consuming to compute locally. That’s…

Protein docking is a cornerstone of molecular modeling, often requiring precision and expertise to achieve meaningful results. One crucial, and often overlooked, step in ensuring docking accuracy is the optimization of range angles — a parameter governing the rotational and…

Efficiently modeling proteins requires understanding their backbone conformations. This can be especially tricky when dealing with strained residues or outliers that don’t conform to expected dihedral angle distributions. Enter the Interactive Ramachandran Plot, a powerful feature in SAMSON that not…

For molecular modelers and protein designers, understanding how proteins are structurally organized is a crucial foundation for any workflow. When dealing with protein structures stored in PDB files, you’ve likely encountered references to their crystal structures and biological assemblies. But…

Biomolecular modelers often face the challenge of understanding large-scale molecular motions like the opening or closing of binding sites. These complex motions are critical for various biological functions, such as ligand binding or protein conformational changes, but traditional computational approaches…

For molecular modelers, balancing precision, performance, and reproducibility in simulations is a constant challenge. If you’re working locally and require a specific version of GROMACS or need to fine-tune your performance parameters, the GROMACS Wizard in SAMSON offers an efficient…

Custom index groups are a valuable tool in molecular dynamics simulations, allowing users to define specific atom groups for analysis, pulling simulations, or advanced setups. If you’re working on complex molecular systems in GROMACS, customizing index groups can significantly improve…