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Cleaning up a molecular system before running simulations is a critical step for ensuring reliable results. One common issue for molecular modelers involves deciding what to do with the crystal waters found in protein structures. While some waters are essential…

Molecular modelers often need to delve deeply into the mechanics of molecular interactions to uncover potential therapeutic strategies or simply to better understand a system of interest. One challenge is studying complex protein motions, such as those of the SARS-CoV-2…

For molecular modelers, one of the most time-consuming challenges can be toggling between different perspectives of a complex molecular structure. Constantly adjusting the viewpoint to focus on specific areas or switch between wide and close-up views can disrupt workflow efficiency.…

For molecular modelers, juggling between multiple views of a structure can be a daunting task. Connecting what you see in a sequence, a structural model, and a 3D view often feels like navigating through a maze. This challenge is especially…

As a molecular modeler, you know that optimizing molecular geometries is a critical step in simulations and molecular design. Achieving stable and realistic structures is paramount, but finding the right tool for this task can be a challenge, especially when…

Managing complex molecular structures can often feel overwhelming for molecular modelers. Workflows require organizing nodes like molecules, residues, atoms, and other details, and balancing efficient navigation, filtering, and modifications can become a challenge. SAMSON’s Document View offers an intuitive way…

For molecular modelers, managing compute-intensive simulations on local machines can be a consistent bottleneck. Running large-scale molecular dynamics simulations like NPT equilibration or production runs often exceeds the resource capacity of personal or even institutional workstations. Fortunately, the GROMACS Wizard…

Potential of Mean Force (PMF) analysis, often seen as a pivotal task in molecular simulations, has long been the cornerstone for understanding reaction processes and free energy changes along reaction coordinates. Yet, for many molecular modelers, turning umbrella sampling data…

For molecular modelers working with Python-based workflows, managing Python packages within an integrated environment can often be challenging. SAMSON, the integrative molecular design platform, provides an elegant solution to this problem with its built-in Python Package Manager. In this guide,…