Author: OneAngstrom

Molecular modeling often involves creating complex structures that need refinement through minimization. But what if you only need to minimize a specific part of your molecule? Minimizing an entire structure can not only be time-consuming but may also lead to…

For molecular modelers juggling multiple systems or conformations, configuring simulations one by one can be a tedious and error-prone task. Batch computations provide a powerful solution, especially for those using SAMSON’s GROMACS Wizard. This article dives into how you can…

For molecular modelers and computational chemists, understanding local packing, solvation structures, or the characteristic interaction distances between atoms or molecules can be critical. The Radial Distribution Function (RDF) is a powerful tool to achieve exactly that. But how do you…

When working with molecular dynamics or structural biology, one common problem molecular modelers face is the challenge of maintaining focus on a specific region or set of atoms in complex simulations. If you’ve ever struggled to keep a clear view…

For molecular modelers working with simulations, customizing your tools to suit your computational needs is essential. When using the GROMACS Wizard in SAMSON, the default GROMACS setup is often sufficient. However, there are cases when you might want to run…

Molecular modelers constantly seek precision and flexibility when visualizing their systems. One common pain point in this context is the need to create smooth, vertical movement in animations to highlight specific structures or dynamics along a vertical axis. The Pedestal…

As a molecular modeler, presenting your data in a visually compelling way is critical for storytelling, whether it’s for research presentations, teaching, or simply showcasing a molecular design. A challenge many modelers face is transitioning smoothly between different regions of…

For molecular modelers looking to simulate membrane-protein interactions, creating lipid layers around proteins can often be a daunting task. The Molecular Box Builder extension in SAMSON offers a powerful yet simple solution for generating lipid membranes, enabling researchers to focus…

Molecular modelers often face the challenge of understanding and modeling the transition paths between different conformations of the same protein. Navigating these transitions can be complex, involving multiple energy states and careful handling of atomic motions. The Protein Path Finder…