SAMSON Blog – Page 354

Launching GROMACS Batch Simulations for Multiple Molecular Conformations

Exploring molecular dynamics for flexible systems often involves analyzing multiple conformations or frames of a molecular system. If you’ve felt the pain of having to simulate each conformation separately — with endless copy-pasting, configuration, and rerunning — you’re not alone.…

How to Create Custom Index Groups for GROMACS Simulations without Writing Selection Scripts

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Custom index groups can be extremely helpful in molecular dynamics simulations, especially when performing detailed analyses or steering parts of your system through advanced scenarios like umbrella sampling or pulling simulations. However, defining these groups using command-line tools and selection…

Easily Find Structural Models with Specific Atom Counts in SAMSON

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When working with large datasets of molecular structures, it can be difficult to focus only on the relevant models for your research. Whether you’re analyzing molecular dynamics, running simulations, or preparing datasets for machine learning, filtering models based on atomic…

Focusing on What Matters: Region-Specific Protein Alignment with SAMSON

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Aligning entire protein structures can be very informative—but sometimes, zooming in on a specific region tells the real story. If you’re modeling conformational variants, analyzing conserved motifs, or aligning flexible regions between homologs, whole-protein superposition might not be enough. That’s…

When Multiple Symmetries Fit: Choosing the Right One in Large Protein Complexes

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One of the recurring challenges in structural biology is simplifying complex protein assemblies without losing key functional insights. This is especially true when setting up simulations or designing targeted mutations. Detecting and working with symmetry in large biological assemblies can…

Selecting Ligands, Receptors, Water and More in One Line

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When working with large molecular systems in SAMSON, it can be hard to focus on just the parts that matter for your task—whether that’s a ligand, a receptor, water molecules, or a visual model. Navigating through hundreds or thousands of…

Avoid Simulation Artifacts: How to Define a Proper Periodic Box for Pulling Simulations in GROMACS

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When setting up a molecular dynamics simulation involving pulling—especially center-of-mass (COM) pulling—most modelers know that choosing a suitable periodic box is essential. However, it’s also one of the most frequent sources of avoidable simulation artifacts due to improper box size…

Quickly Find Structural Groups Based on Partial Charges in SAMSON

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When working with large molecular systems, locating structural groups with specific charge distributions can be a tedious task. Whether you are investigating charge transfer, analyzing molecular interactions, or debugging unexpected electrostatic properties, you often need to filter and select structural…

Building Carbon Nanotubes in Minutes with SAMSON’s Pattern Editors

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Designing carbon nanotubes (CNTs) atom by atom used to be a complex and time-consuming task. For researchers and students working in nanotechnology and materials science, this process often involved manually aligning atomic rings, estimating spatial parameters, and tweaking bonding arrangements.…

Quickly Isolate the Files You Need in SAMSON with NSL

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When working on complex molecular systems, one of the recurrent frustrations for computational scientists is managing and filtering through large numbers of files inside a project. From simulation results to experimental structures, projects often include multiple file nodes that must…