Author: OneAngstrom

One of the significant challenges faced by molecular modelers is the tedious process of preparing multiple protein structures for downstream workflows, such as docking simulations, molecular dynamics, or structure validation. What if you could automate the preparation of numerous PDB…

If you’ve ever worked with molecular modeling, you know how critical it can be to monitor a molecule’s shape changes over a particular trajectory or pathway. Understanding the shape anisotropy – or how much a shape deviates from being perfectly…

For molecular modelers and researchers working with protein dynamics, tracking backbone-state changes over time can be a challenging yet crucial task. Whether you’re diving into protein folding studies, monitoring domain transitions, or studying unstructured regions, efficiently summarizing such structural data…

Molecular modeling workflows can sometimes hit roadblocks due to hardware compatibility issues. For users installing SAMSON, one common challenge arises when working with Intel graphics cards. If you’re facing this issue, this guide will help you understand the problem and…

When studying molecular pathways, understanding energy distributions can often be a challenging task. For molecular modelers, identifying low-energy basins, high-population regions, and transition states is a crucial step in analyzing and designing systems. The Energy Landscape analysis in SAMSON’s Path…

For molecular modelers, ensuring that a system’s density stabilizes before diving into full production simulations is a critical yet intricate step. NPT Equilibration, which operates under constant Number of particles, Pressure, and Temperature, is a cornerstone process in molecular dynamics.…

In molecular modeling, visual clarity is crucial, especially when presenting or analyzing complex systems. One of the common challenges modelers face is emphasizing specific structures or regions within a molecular model, without permanently altering their appearance. This is where SAMSON’s…

As anyone working in molecular modeling knows, precision is key. But we all make mistakes or wish to explore alternate approaches to a structure without fear of losing progress. Whether you’re modifying molecular structures, running simulations, or designing custom molecules,…