SAMSON Blog – Page 115

A Practical Guide to Covalent Docking with the FITTED Suite in SAMSON

Covalent docking is a powerful strategy in structure-based drug design, especially when targeting active sites with known reactive residues. However, setting things up properly — from hybridization to binding site specification — can be a major source of friction for…

Got a GROMACS Trajectory? Here’s How to Use It for Umbrella Sampling in One Go

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Umbrella Sampling is a powerful technique for calculating free energy profiles along reaction coordinates, but setting it up can be time-consuming, especially when using data from existing trajectories. If you’re a molecular modeler with a finished GROMACS trajectory from a…

Why Your Molecular Simulations May Fail Without NVT Equilibration

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One of the most common frustrations that molecular modelers encounter is when a simulation runs, but the system behaves erratically—either heating up quickly or displaying unstable behavior. A major reason? Skipping or misconfiguring the NVT equilibration phase. In molecular dynamics,…

Target Specific Atoms by Geometry in SAMSON: A Practical Guide for Molecular Modeling

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One of the recurring challenges in molecular modeling is selecting atoms based on structural properties – particularly geometry. For instance, identifying atoms with tetrahedral geometry can be important for understanding chemical reactivity, assigning force field parameters, or preparing input for…

Make Models Fade Naturally with the Disappear Animation in SAMSON

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In molecular modeling, visual clarity is key. Whether you are preparing educational content, publishing research, or just trying to better understand a complex structure, being able to control what appears and disappears from your view can make a big difference.…

From Molecules to Meshes: Exporting 3D Geometries with SAMSON

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Molecular modelers often want to export their models as 3D geometries—for 3D printing, visual design, AR/VR environments, or integration into other platforms. But not every molecular modeling platform makes this easy. Fortunately, SAMSON provides a clear path for exporting molecular…

When You’re Stuck in Molecular Modeling, Try This

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Molecular modeling can be exciting and rewarding, but getting started—or even diving deeper into a complex workflow—can often feel overwhelming. Maybe you want to analyze protein-ligand binding, simulate conformational changes, or build molecular systems from scratch. Tools like SAMSON offer…

Effortless Scientific Storytelling: Using Background Animations in SAMSON Presentations

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Creating clear, engaging visual presentations of molecular systems is a daily challenge for many researchers, educators, and communicators in molecular science. Whether presenting results at a conference or preparing animations for student lectures, one of the recurring pain points is…

Making Molecular Highlights Stand Out with the Pulse Animation

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When you’re presenting a molecular system, clarity can make a big difference. Whether you’re teaching, explaining your research, or sharing results with collaborators, the ability to focus viewers’ attention on specific parts of a model is essential. This is where…

Seeing Molecules Clearly: A Guide to Visual Models in SAMSON

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Understanding molecular systems is often about more than just numbers—it’s about seeing the structure, interactions, and properties in ways that make patterns and behaviors intuitively clear. That’s where visual models in SAMSON come in. For molecular modelers, one recurring challenge…