OneAngstrom – Page 15

Avoid Jumpy Movements When Animating Molecular Systems

When presenting complex molecular transformations or simulations, one of the most frustrating problems molecular modelers face is jittery or discontinuous motion. Whether you’re creating animations to communicate results or to better understand molecular processes, the key to clear, compelling molecular…

A Quick Path to PMF Profiles with WHAM in GROMACS Wizard

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Understanding the free energy landscape of a biomolecular system is key to gaining insights into processes like binding, folding, and conformational changes. One widely used approach for this is Potential of Mean Force (PMF) analysis using the Weighted Histogram Analysis…

When Bonds Break: Handling Topology Changes in Interactive Molecular Modeling

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One of the most common hurdles in molecular modeling arises when a user attempts to edit a structure interactively and ends up frustrating the system—bonds don’t break, new atoms refuse to connect, or the energy landscape becomes unstable. If you’ve…

Make Visual Selection Easier in SAMSON with Render Preset Attributes

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When working with complex molecular systems, molecular modelers often have to visually isolate specific parts of their structures using consistent rendering styles. This is especially useful when preparing figures for publications or presentations, or when exploring specific substructures during a…

Simulating Multiple Conformations at Once: A Time-Saving Workflow for Molecular Modelers

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One of the recurring challenges in molecular modeling is evaluating how different conformations of a single molecular system behave under identical simulation conditions. Whether you’re performing Umbrella Sampling or exploring conformational variability, setting up individual simulations for each structure can…

Keeping Your Focus: Following Atom Groups Without Moving the Camera

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When analyzing complex molecular systems, it is often necessary to track the movement of a specific group of atoms—perhaps a binding site, a ligand, or a key structural motif—during a simulation trajectory. However, rotating and translating the camera manually to…

Make Molecules Appear Right When You Need Them

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When preparing molecular animations for presentations or publications, timing is everything. A common challenge in molecular modeling is making important molecules or structural elements appear exactly when they become relevant—without fading effects or complex scripting. If you’ve ever struggled with…

Focus Your Molecular Optimization: How to Minimize a Single Molecule in SAMSON

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When working on complex molecular systems, it’s common to want to optimize the geometry of just one molecule without affecting the rest of the scene. But doing this selectively — without unintentionally altering neighboring structures — can be tricky. SAMSON…

How to Filter and Organize Your Camera Nodes in SAMSON

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When working on complex molecular models or reaction simulations, controlling the viewpoint can be as important as the data itself. Molecular modelers often resort to creating multiple camera nodes to represent different perspectives, highlight specific molecular components, or prepare illustrative…

Revisiting Molecular Journeys: How to Play Trajectories in Reverse in SAMSON

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Molecular modelers often need to analyze conformational transitions, loop back through molecular motions, or visualize symmetry in paths taken by atoms or groups in simulations. While viewing trajectories forward is standard, playing them in reverse can be surprisingly valuable: it…