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Properly setting up periodic boundary conditions and selecting the right unit cell are key to conducting efficient molecular simulations. For molecular modelers using GROMACS, understanding how to choose the most appropriate space-filling unit cell not only improves simulation accuracy but…

Protein structures can adopt multiple conformations, critical for understanding their function in biological systems. Modeling a smooth, realistic transition path between two such conformations can be a challenge for molecular modelers, especially under time constraints or when aiming for high…

When working on molecular models, conveying complex information often requires dynamic visual presentations. Yet, managing what should be visible and when during animations can be a source of frustration. This is where SAMSON’s Hidden animation effect steps in, offering a…

For molecular modelers, learning a new tool can sometimes be a daunting task. Whether you’re a beginner or an experienced scientist exploring the SAMSON molecular design platform, finding practical guidance is crucial. One powerful feature that can make your journey…

Molecular modeling often involves intricate edits, and making mistakes along the way is inevitable. Fortunately, SAMSON provides a powerful History feature that allows you to manage undoable operations efficiently, saving both time and effort during your design workflows. What is…

Molecular modeling often involves navigating the complexities of atomic interactions, bond formation, and structural modifications. A recurring challenge for modelers is the ability to perform these tasks seamlessly while visualizing and interacting with the molecular system in real-time. This is…

For molecular modelers, refining protein structures often feels like navigating a maze. Ensuring residues adopt energetically favorable conformations is crucial for reliable simulation and accurate modeling results. Fortunately, the Interactive Ramachandran Plot Extension in SAMSON provides a streamlined solution to…

Umbrella Sampling is a powerful method frequently used by molecular modelers to calculate free energy profiles along specific reaction coordinates. However, the most time-consuming step in this process often involves preparing initial conformations and setting up simulations correctly. If you’ve…