Preparing a coarse-grained molecular simulation can seem like a daunting task, especially when ensuring all the key elements—like periodic boxes, solvents, and ions—are in place. If you’re working with the GROMACS Wizard on SAMSON, a versatile integrative molecular design platform,…

One of the core challenges faced by molecular modelers is conducting reliable and efficient non-covalent docking workflows. Whether you’re designing a drug molecule or trying to analyze protein-ligand interactions, a robust and user-friendly solution can make the process significantly smoother.…

As molecular modelers, we often face the challenge of creating clear and engaging presentations for our work. In animations, particularly those depicting molecular changes or processes, control over visibility is a key factor. Enter the Shown animation in SAMSON, a…

Many molecular modelers face the challenge of understanding how structural imperfections, such as defects, influence the properties of crystals. This blog post provides a practical guide to exploring and visualizing defects in diamond crystal structures using the Crystal Creator Extension…

For molecular modelers, customizing workflows is often essential to address specific needs for simulations and analyses. When using GROMACS, the default index groups generated by the tool are helpful, but they may not cover all cases. For example, what if…

One of the common challenges molecular modelers face is efficiently manipulating and editing molecular structures without disrupting complex topologies. Whether it’s creating or breaking covalent bonds, adjusting bond orders, or redefining atom types, maintaining a seamless workflow can be challenging.…

Tracking the movement of molecules during molecular simulations, such as ligand unbinding or macromolecular conformational changes, is essential for understanding biological processes. However, visualizing this motion effectively can be a challenge for molecular modelers. The Pathlines extension in the SAMSON…

Accurate measurements are at the heart of many molecular modeling tasks, whether you’re analyzing bond lengths, angles, or torsional configurations. In SAMSON, the integrative molecular design platform, the Measure editor is your go-to tool for precise and informative measurements. But…

For molecular modelers diving into advanced Molecular Dynamics (MD) simulations, center-of-mass (COM) pulling is often essential. However, the setup process—ensuring the system is ready, the pulling parameters are correctly defined, and the model is prepared—can feel like a daunting task.…