SAMSON Blog – Page 131

Avoid Ligand Confusion: Correctly Selecting Ligand Atoms in Ligand Path Finder

One of the most common setup issues encountered by molecular modelers working on protein-ligand interactions is an incorrect definition of the ligand itself. This can lead to inaccurate path predictions, unexpected energies, and even failure of the algorithm to find…

A Simple Way to Play Trajectories in Reverse with SAMSON

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When analyzing molecular structures and motions, it’s often helpful to step back—literally. While forward trajectories offer valuable insights, playing molecular paths in reverse can highlight subtle interactions, simplify comparisons, or illustrate transitions between conformations more clearly. This is especially useful…

Following Atoms with the Camera: A Simple Way to Frame Better Molecular Animations

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Creating molecular animations can be incredibly powerful when trying to convey structural mechanisms or simulation results — but getting the camera to follow atoms precisely in 3D space is often a challenge. Whether you’re highlighting a docking process or zooming…

How to filter molecular bonds by length in SAMSON’s Node Specification Language

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When working with molecular models, identifying bonds of specific lengths is often essential. Whether you’re analyzing structural changes, refining a force field, or creating visualizations that focus on specific bonding regimes, quickly filtering for bond lengths can save a lot…

Struggling with molecular file types? Here’s how SAMSON handles them.

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One of the most persistent issues that molecular modelers face is dealing with the variety of file formats present in computational chemistry and structural biology. Between .pdb, .mol2, electron density maps, and dozens more, managing the import process often becomes…

Duplicating Molecular Structures Without Scripts or Spreadsheets

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As molecular modeling projects grow in complexity, manually duplicating and arranging molecular structures can quickly become tedious. Whether you’re assembling a nanotube from scratch or building repeating motifs in materials science or biomolecular models, the goal is the same: replicate…

Why Applying P-NEB to a Path Is Often the Smartest Choice

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When modeling molecular systems, understanding how a molecule transitions from one conformation to another can be crucial. These transition paths often characterize reaction mechanisms, ligand unbinding, or conformational changes. However, extracting precise transition information can be computationally expensive and time-consuming,…

Avoiding Common Pitfalls When Preparing Ligands for Docking

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Preparing ligands for docking can sometimes feel like a guessing game: are all hydrogen atoms present? Are rotatable bonds under control? Is the molecule properly minimized? If you’ve found yourself spending more time troubleshooting input data than analyzing results, you’re…

Easier Umbrella Sampling from Existing Trajectories in SAMSON

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Generating initial conformations for umbrella sampling can be time-consuming, especially for researchers who already have a simulation trajectory and want to reuse it efficiently. If you’re using SAMSON’s GROMACS Wizard, there’s a streamlined and visual way to set this up…

Setting Up UFF Simulations in SAMSON Without the Guesswork

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Setting up a molecular mechanics simulation can feel like preparing for a journey with no map—especially when working with customizable force fields like the Universal Force Field (UFF). If you’ve ever hesitated because you weren’t sure how to initialize UFF…