SAMSON Blog – Page 488

How to Correctly Define a Simulation Box for COM Pulling

When preparing molecular dynamics simulations that involve center-of-mass (COM) pulling — such as separating chains in a protein complex — one of the most common sources of error is the incorrect definition of the simulation box. The consequences? Unexpected interactions…

Trouble Seeing Labels in Your Model? Here’s a Precise Way to Control Visibility

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When working with complex molecular designs in SAMSON, it’s easy to lose track of labels—especially when shifting between different states, selections, or visualization settings. If you’ve ever had the frustrating experience of wondering why a label isn’t visible (or why…

Changing Simulation Parameters Without Breaking Your Workflow

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If you’ve ever felt the friction of customizing molecular dynamics (MD) simulations in GROMACS, you’re not alone. Manually editing .mdp files, searching for the right flags, worrying about compatibility—all of this can slow down your work and distract you from…

Filtering Molecular Paths by Atom Count in SAMSON

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When working with complex molecular models, it’s common to want to isolate specific structural paths—like chains, ligands, or pathways—that meet certain criteria. One frequent need is to find paths based on their size, that is, the number of atoms they…

Choosing Initial Conformations for Umbrella Sampling Without Guesswork

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Setting up an umbrella sampling simulation can be a tedious process, especially when trying to decide which snapshots to use as initial conformations. Molecular modelers often find themselves manually selecting frames from trajectories or trying to estimate proper spacing between…

Making Sense of Bond Types in Molecular Models (Without the Guesswork)

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When you’re inspecting or designing molecular systems, it’s easy to overlook how deeply bond types influence molecular behavior. Whether you are analyzing a drug molecule, building a polymer, or examining a crystal structure, the type of bond—single, double, aromatic, and…

Quickly Filter and Control Notes with NSL in SAMSON

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As molecular modelers, we often use annotations—or note nodes—to clarify structures, mark regions of interest, or collaborate with others. However, in large models, these notes can become overwhelming unless we have a fast way to search, filter, and toggle their…

Stop Getting Lost in Molecular Models: How Document View Helps You Stay Organized in SAMSON

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Molecular modelers often juggle multiple structures, simulations, and scripts all at once. Keeping track of everything inside a complex molecular modeling project can quickly become overwhelming—especially when dealing with large biomolecular systems or comparing multiple candidate structures. That’s where the…

Manually Build Carbon Nanotubes in SAMSON with Pattern Editors

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Carbon nanotubes (CNTs) are widely used in nanotechnology, materials science, and molecular simulation. But for many molecular modelers, designing a CNT manually—with precise atomic control—can be tedious and unintuitive. Whether you’re prototyping a custom topology or studying interactions at the…

Saving Hours: How to Prepare Hundreds of Protein Structures at Once with SAMSON

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If you’ve ever worked on a large-scale protein modeling or virtual screening project, you’ve probably experienced the tedious task of preparing many protein structures for simulation or docking. Downloading PDB files, cleaning them, removing unwanted molecules, and adding missing atoms…