In molecular dynamics simulations, ensuring your system is neutral is not just a best practice—it’s essential for accurate results. If you’re new to the topic or revisiting the workflow for pulling simulations, this guide will provide you with a clear…

Have you ever wondered how to seamlessly document atom trajectories and paths while working on molecular models? Capturing these intricate movements can be challenging, yet it’s an integral part of presenting molecular simulations or designing animations that communicate your research…

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…