Uncategorized – Page 389

From Design to Simulation: Exporting DNA Nanostructures for oxDNA in Adenita

Designing DNA nanostructures is only half the task for molecular modelers interested in simulations. Once the geometry is ready, the challenge becomes how to export that design for computational analysis. If you work with coarse-grained molecular dynamics, you’re likely using…

Let Your Molecules Fade Out Gracefully with the Disappear Animation

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In molecular modeling, clarity is key. Whether you’re presenting a simulation, building an educational video, or simply exploring complex biomolecular structures, drawing attention to specific components while minimizing distractions can greatly improve communication. One common challenge modelers face is how…

Avoiding Solvent Clashes in Coarse-Grained Simulations with GROMACS Wizard

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Setting up a coarse-grained (CG) system for molecular dynamics simulations can save time and computational resources, but comes with its own challenges. One such challenge — often overlooked by beginners — is related to how solvent molecules are added to…

Quickly Select Aromatic Carbons (and More) with Atom Attributes in NSL

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Molecular modeling often involves selecting very specific subsets of atoms. For instance, you might want to isolate only aromatic carbons, or exclude metal atoms from a visualization. These selections can quickly become tedious—unless you know how to use the Node…

Avoid Repeating Simulations by Recording Atom Paths in SAMSON

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When working on molecular simulations or structural rearrangements, animation workflows can become repetitive and time-consuming. A common challenge for molecular modelers is ensuring that once they achieve the right animation involving atom movements—for example, docking, simulated dynamics, or manual manipulation—they…

Making Molecules Disappear: A Visual Trick for Clearer Presentations

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One of the constant challenges faced by molecular modelers is simplifying complex molecular scenes for presentations or animations. Whether it’s to highlight a reaction site, declutter overlapping strands, or direct attention to a specific structure, controlling visibility is a key…

A Practical Guide to Aligning Molecular Structures in SAMSON

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Aligning molecular structures may sound simple, but anyone working at the atomic level knows that precision matters—whether you’re comparing docking poses, preparing figures, or building assemblies. If you’ve ever wrestled with rotating, translating, and centering molecules manually, this post is…

From 2D to 3D: Instantly Visualize Analogs with the SMILES Manager

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When exploring new molecules in drug discovery or materials science, seeing the molecule in 3D isn’t a luxury—it’s a necessity. However, for many molecular modelers, converting a generated 2D molecular structure (e.g., from a SMILES code) into its 3D counterpart…

Creating Custom Index Groups for COM Pulling in GROMACS Wizard

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When setting up a molecular dynamics simulation involving pulling or restraining specific molecular parts, having precise control over which atoms belong to which group is crucial. This is especially important in center-of-mass (COM) pulling simulations where specifying exactly which atoms…

Filtering Molecular Conformations by Atom Count in SAMSON

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When analyzing molecular systems, it’s often useful—if not essential—to filter or select specific molecular conformations based on the number of atoms they contain. This might be relevant when comparing various snapshots during a simulation, isolating smaller or larger fragments, or…