Author: OneAngstrom

For molecular modelers, achieving a stable and controlled system temperature during simulations is a critical step. Without proper temperature stabilization, subsequent steps, like density equilibration or production simulations, might fail or lead to unreliable results. This is where the NVT…

If you're a molecular modeler, you know that clear, effective visualization is crucial when presenting complex molecular structures or simulations. One challenge that often arises is selectively making specific parts of your molecular model visible during an animation. SAMSON's Shown…

Creating complex, nanoscale molecular architectures is often a challenge for molecular modelers due to the precision and repetitive tasks involved. Whether you’re designing nanotubes, arranging biomolecular assemblies, or developing material prototypes, SAMSON’s Pattern Editors can transform what often feels like…

Molecular modeling often involves exploring variations of a molecule to find optimal properties, improve interactions with targets, or test new hypotheses. One effective approach to achieve this is Positional Analogue Scanning (PAS), which lets you systematically modify specific parts of…

One of the crucial steps in molecular modeling and simulations is preparing your protein system. Preparing your protein correctly can significantly improve the accuracy of your results, prevent potential errors, and save valuable time in your workflow. In this tutorial,…

Molecular modelers often encounter a common obstacle when preparing systems for simulation: deciding which water molecules to keep and which to remove. While certain waters play functional roles in biological systems, many others add unnecessary complexity. The GROMACS Wizard in…

When working on molecular modeling tasks, one common bottleneck is optimizing transition paths between conformational states. This is particularly challenging when the initial paths are rough or unrefined — a scenario many molecular modelers face when striving to predict physically…

Modeling molecular transitions often involves determining accurate pathways between two states—say, a protein-ligand binding event or a conformational change of a macromolecule. However, the challenge lies in refining these paths to obtain physically meaningful, optimized transitions that can reveal key…