SAMSON Blog – Page 100

Quickly Isolate Specific Node Groups in SAMSON: A Practical Guide to Using Selection Attributes

When working on complex molecular models, isolating specific subsets—such as ligands, modified residues, or structural domains—can be a major time-saver. The Node Specification Language (NSL) in SAMSON provides a robust way to target these subsets using attributes, and in this…

Making Sense of Pressure: A Practical Guide to NPT Equilibration with GROMACS Wizard

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One of the most common challenges in molecular dynamics simulation is ensuring that a system reaches realistic density and pressure conditions before launching a production run. If you’ve ever struggled with fluctuating densities or simulation artifacts due to poorly equilibrated…

Quickly spot sampling gaps in PMF calculations using GROMACS Wizard

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Running umbrella sampling simulations is a major step in estimating free energy profiles along reaction coordinates. But for molecular modelers, a recurring problem is not knowing whether the simulation data you’ve generated is enough—or balanced enough—to perform reliable Potential of…

Tired of Repeating Tasks in Molecular Modeling? Let SAMSON AI Script It for You.

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Many molecular modelers often find themselves repeating the same actions: translating atoms, computing molecular properties, or building small interactive tools. When done manually or hardcoded repeatedly into Python scripts, these tasks can become tedious and time-consuming. If this feels familiar,…

Choosing the Right Input for NVT Equilibration in GROMACS Wizard

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When setting up molecular simulations, one common challenge is managing simulation input data between steps. It can be surprisingly easy to misplace a file, use the wrong structure, or re-run calculations that were already done, simply because of input mismatches.…

Saving Your Molecular Models: A Quick Guide to Exporters in SAMSON

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If your work involves molecular modeling, visualization, or simulation, you’ve likely run into the need to export your structures or visuals to share results, perform additional analysis, or publish your work. This step, though often perceived as simple, can cause…

When Hiding Is Better Than Fading: A Simple Trick in Molecular Animations

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Communicating molecular insights visually is one of the most powerful ways to convey structure-function relationships, simulation results, or molecular mechanisms. Yet, some subtle visualization choices can make or break the clarity of your output. Have you ever tried to make…

Solvating Coarse-Grained Systems in GROMACS Wizard: Avoiding Common Pitfalls

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Preparing a coarse-grained (CG) system for molecular dynamics (MD) simulations can often be frustrating when solvent models behave unexpectedly. One common issue many molecular modelers face is improper solvation due to van der Waals (vdW) clash errors or insufficient solvent…

Building Repetitive Molecular Structures with SAMSON’s Pattern Editors

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Designing nanoscale systems often requires repeated arrangements of atoms or molecular fragments—think helices, nanotubes, or crystal-like lattices. Yet, replicating and aligning these geometries manually can quickly become tedious and error-prone. That’s where SAMSON’s Pattern Editors come in: intuitive tools that…

Precise Molecular Alignment in SAMSON Without Scripting

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Aligning molecular structures in 3D space is a common task in molecular modeling workflows. Whether you’re preparing a system for analysis, visualizing structures together, or setting up simulations, the ability to quickly and accurately align molecules along reference axes or…