OneAngstrom – Page 92

Running GROMACS Simulations in the Cloud Without Installing Anything

Running molecular dynamics (MD) simulations often involves long preparation steps, software installation and compilation, and configuration of local computing resources. If you’re working in a constrained environment (e.g., a classroom, a shared lab PC, or just traveling with a lightweight…

Quick Visual Breakups: Using the Undock Animation in Molecular Presentations

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Communicating molecular interactions often involves not only showing how components come together, but also how they come apart. Whether you’re demonstrating ligand departure, the dissociation of a protein complex, or just separating structural components in a clear visual, choosing the…

Managing Cloud Simulations More Easily with SAMSON’s Job Manager

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Running complex simulations like molecular dynamics with GROMACS or predicting protein structures with AlphaFold often means dealing with long runtimes and high computational requirements. These tasks can significantly slow down your local system or require powerful hardware that is not…

When Steepest Descent Isn’t Enough: A Simple Way to Speed Up Geometry Optimization with FIRE

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In molecular modeling, geometry optimization is fundamental—whether you’re prepping a structure for simulation, cleaning up PDB data, or simply hunting for a local energy minimum. Yet, many continue to rely on the steepest descent algorithm, even when faster, more suitable…

Choosing Discrete Color Palettes That Make Molecular Models Clearer

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When working with complex molecular systems, properly distinguishing between structures, regions, or types of data is critical. One challenge that comes up often in molecular modeling: how do you make your models visually clear and easy to interpret at a…

How to Quickly Select and Filter Cameras in SAMSON Using NSL

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Working with multiple cameras inside a complex molecular system can feel overwhelming. In integrative modeling platforms like SAMSON, cameras help visualize the system from different perspectives—especially useful during animation, scene capturing, or scientific reporting. However, selecting and managing these cameras…

Saving Time with Custom Index Groups in GROMACS Wizard

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If you’ve ever needed to define custom index groups in GROMACS, you probably know how time-consuming it can be to manually select atoms, residues, or regions of interest using command-line tools. Whether you’re preparing systems for umbrella sampling, pulling simulations,…

Bringing Molecules Into Focus: Customizing Rendering Preferences in SAMSON

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Visual clarity is often underestimated in molecular modeling. When working on complex structures, subtle differences in depth, lighting, and background can lead to misinterpretations or eye fatigue over long sessions. If you’ve ever struggled to perceive spatial relationships in your…

Quickly Managing Label Visibility in Molecular Models

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When working with complex molecular models, labels can help interpret specific molecular features—residues, atoms, functional groups, and more. But when there are too many of them, labels may hinder rather than help. Efficiently toggling label visibility becomes essential, especially when…

Making NVT Equilibration Easy: Automatically Load Inputs in SAMSON’s GROMACS Wizard

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One of the recurring pain points for computational molecular scientists is managing the multiple input and output files between different simulation steps. This becomes especially cumbersome when performing sequential operations like energy minimization followed by NVT and NPT equilibrations, where…