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Ligand parametrization is often a critical and complex step in molecular modeling and simulations, especially when preparing systems for tools like GROMACS. Ensuring compatibility with specific force fields and correctly setting up input files can be time-consuming and challenging. Here,…

Working on molecular models often requires pinpointing specific regions with crystal-clear precision. Whether adjusting intricate details or focusing on specific areas without altering the perspective of your view, staying in control of the zoom becomes an essential part of the…

In molecular modeling, efficiently exporting atomic trajectories is critical, whether for reaction coordinate studies, free energy calculations, or observing the movement along ligand pathways. The Export Along Paths extension in SAMSON addresses this pain point by providing a streamlined way…

Building large molecular systems efficiently and accurately can sometimes feel like solving a puzzle with too many pieces. Whether designing nanotubes for nanotechnology, biomolecular assemblies for biological simulations, or modeling complex materials for material science, creating repetitive structures is an…

Configuring molecular dynamics (MD) parameters is one of the most significant aspects of running successful production simulations with the GROMACS Wizard in SAMSON. For newcomers to molecular modeling or even experienced modelers looking to refine their workflows, getting the parameters…

DNA nanostructures offer immense opportunities for structural and functional innovation in nanotechnology. However, starting every nanostructure from scratch can be overwhelming and time-consuming for researchers and modelers. Luckily, Adenita, an extension for SAMSON, makes this process far more efficient by…

As a molecular modeler, keeping track of specific zones within a molecular system can be a challenge, especially when analyzing complex molecular dynamics or trajectories. The Look at atoms animation in SAMSON offers a simple yet effective solution by automatically…

For molecular modelers, efficiently separating groups of atoms, meshes, or structural nodes can often present a significant challenge. Whether you are working on ligand-receptor interactions, generating molecular presentations, or simulating animations, achieving clarity in visualization is paramount. The Undock animation…