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This section is a part of the GROMACS Wizard tutorial. This tutorial demonstrates how to perform batch computations using GROMACS Wizard for a set of initial conformations of a single molecular system. To use an existing trajectory, load it in SAMSON. You can also create a trajectory or a set of conformation in SAMSON using various tools: editors (Move editors, Twister), various extensions (AutoDock Vina Extended, Normal Modes Analysis, Ligand Path Finder, Protein Path Finder, protein-protein docking with Hex, etc.), animations (Dock,…

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This section is a part of the GROMACS Wizard tutorial. This tutorial demonstrates how to compute the Potential of Mean Force (PMF) using the Weighted Histogram Analysis Method (WHAM) in GROMACS Wizard. Switch to the WHAM Analysis tab in GROMACS Wizard. Choose the project path or click on auto-fill if the previous project you ran was the Umbrella Sampling simulation. The project folder might be a result of the batch computation, and it needs to contain numbered subfolders each containing simulation…

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Introduction Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful and versatile analytical tool extensively used in chemistry and biology to determine the structure of molecules, including protein-ligand complexes. Unlike X-ray crystallography that requires crystalline samples, NMR spectroscopy can analyze molecules in solution, closely mimicking physiological conditions. This makes NMR particularly suited for studying interactions between proteins and ligands. This tutorial demonstrates how to use the integration of NMR2, a method developed by Prof. Dr. Julien Orts from Vienna University, into…

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This is Part V of What’s new in SAMSON 2023 R1, the release notes for SAMSON 2023 R1. ✅ New Pricing Structure To reflect the major changes introduced in this SAMSON release, we have updated and simplified our pricing structure, and it gives you even more insane value than before! First, the Free Starter Plan lets you do even more than before, with SAMSON AI, Molecular Cycles, Integrated Python Development Environment, and so much more! Second, to make things simpler,…

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This is Part IV of What’s new in SAMSON 2023 R1, the release notes for SAMSON 2023 R1. 💡 Interface redesign, and so much more! SAMSON 2023 R1 features a major redesign of the interface to offer a more streamlined experience, with numerous quality-of-life improvements. Context toolbar Now, when selecting nodes in SAMSON, a new context toolbar gives you direct access to the frequently used commands. The toolbar makes it possible to rapidly access SAMSON AI, operate on the selection…

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This is Part III of What’s new in SAMSON 2023 R1, the release notes for SAMSON 2023 R1. Integrated Python Development Environment 🐍 The Future of Research and Collaboration with SAMSON Prepare for a radical shift in the way you conduct and share research with SAMSON: the new release goes far beyond the boundaries of typical molecular modeling platforms to bring you a fully integrated Python Development Environment. This is not just an addition; it’s a transformation that empowers you…

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This is Part II of What’s new in SAMSON 2023 R1, the release notes for SAMSON 2023 R1. Molecular Cycles 🌟: Studio-Quality Visuals Right Inside SAMSON The SAMSON 2023 R1 release brings another groundbreaking feature that will redefine your visualization experience. We’re proud to announce the integration of the Cycles Renderer from Blender, a renowned, open-source 3D computer graphics software, into SAMSON. Studio-Quality Rendering for Images and Animations For the first time in SAMSON, you can now have stunning, studio-quality…

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This is Part I of What’s new in SAMSON 2023 R1, the release notes for SAMSON 2023 R1. SAMSON AI ✨: Your Next-Generation Modeling Assistant We are thrilled to announce one of the most exciting features in SAMSON 2023 R1: SAMSON AI, a cutting-edge assistant powered by an LLM-based architecture integrating the OpenAI API. SAMSON AI isn’t just another chatbot; it’s an intelligent agent designed to make your molecular modeling experience as intuitive, efficient, and rewarding as possible. Here’s how…

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In this small article, we provide a brief introduction about the way the SARS coronavirus 2 (SARS-CoV-2) operates, and we provide results of our computations of the motion of its spike from its closed state to its open, receptor-binding state. Introduction The SARS coronavirus 2 (SARS-CoV-2) – the virus that causes the COVID-19 disease – has transmembrane spikes (S proteins on the image below) attached to its lipid membrane. It is because of these spikes – their relatively large number –…

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Molecular Box Builder makes it possible to construct systems by inserting molecules in a box or filling a box with molecules. The Molecular Box Builder app can be found in the App menu > Assembly or via the “Find everything” (Shift+E) in the top-right corner of SAMSON. Setting a molecule Select a system with which you would like to populate a box in the Document view or in the Viewport. The system can be a single molecule or a set of molecules…

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