SAMSON Blog – Page 56

Finding the Right Tools for Molecular Modeling in the SAMSON Marketplace

One of the biggest challenges faced by molecular modelers today is finding the right combination of tools without switching constantly between different software environments. If you’ve ever wished for a seamless way to expand your modeling capabilities directly within your…

Conformations vs. Paths: A Time-Saving Tip When Using P-NEB

OneAngstrom

Finding saddle points and minimum energy paths (MEPs) between molecular conformations can be computationally expensive. The Parallel Nudged Elastic Band (P-NEB) method in SAMSON is designed to optimize such transitions by refining intermediate images along a proposed path. But depending…

Before You Plan Protein Transitions, Minimize First — Here’s How

OneAngstrom

When modeling conformational transitions in proteins, small details can lead to big differences in results. One frequently overlooked step is proper energy minimization before running any transition pathway planning. Skipping this step can introduce artificial forces, limit convergence, or worse…

Constrained Simulations in SAMSON: Ensuring Realistic Molecular Motions

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One of the more subtle challenges in molecular modeling is producing simulated motions that are both physically realistic and computationally efficient. Molecular dynamics can rapidly become inaccurate when atoms move in ways that break the constraints imposed by molecular structures…

Building a Lipid Layer Around a Protein Without Manual Guesswork

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Preparing membrane-protein systems for simulation is a task that molecular modelers regularly face, especially when modeling transmembrane proteins. However, manually inserting lipids and ensuring proper alignment around a protein can be time-consuming and error-prone. If you’ve ever tried to construct…

Framing Molecular Structures with the Orbit Camera in SAMSON

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Molecular modeling often requires precise visualization to communicate structural insights clearly — whether in academic papers, presentations, or team meetings. But framing your molecular system from the right angles can be time-consuming, especially if you’re repeatedly adjusting views to get…

Avoiding Reaction Coordinate Gaps in PMF Analysis with GROMACS Wizard

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Running umbrella sampling simulations is only part of the story in calculating a Potential of Mean Force (PMF). A common challenge molecular modelers face is realizing—too late—that parts of the reaction coordinate space were not well covered, leading to unreliable…

Tired of Rebuilding Molecular Visualizations? Save Time with Custom Visual Presets

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One of the most common frustrations in molecular modeling is constantly reconstructing the same types of visualizations: highlighting ligands, showing ribbons for proteins, zooming in on active sites, choosing color schemes, and setting up camera perspectives. When models become complex,…

Make Your Molecules Gently Vanish in SAMSON

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When preparing animations for scientific presentations or teaching materials, molecular modelers often face a common challenge: how to clearly show the removal or disappearance of molecular parts without making the transition feel abrupt. Using simple hide/show toggles can break the…

Easily Select Chains by Residue Count in Your Molecular Models

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A common challenge when working with complex biomolecular systems is efficiently identifying and selecting chains based on their characteristics. Suppose you’re analyzing a protein–protein interaction, or refining a molecular assembly, and want to focus only on chains that are sufficiently…