SAMSON Blog – Page 17

Saving Time with Custom Index Groups in GROMACS Wizard

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…

Filtering molecular folders by atom counts in SAMSON

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When working with complex molecular systems, it’s not unusual to accumulate a large number of molecular folders—each potentially comprising various atoms, chains, and structural features. This can make it difficult to quickly isolate the folders you want to work with.…

Make Your Molecules Pop: Using Visual Presets in SAMSON

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If you’ve ever spent hours building a molecular model only to end up with a blurry, color-confusing visual that doesn’t quite communicate your findings, you’re not alone. For molecular modelers, visually conveying structure and interaction is often as important as…

What Happens After You Click “Simulate”? Understanding Your GROMACS Results

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Molecular modeling can be a meticulous process, and when a production molecular dynamics (MD) simulation wraps up, there’s often a big question: What did it produce, and how do I interpret it? The GROMACS Wizard in SAMSON makes life a…

Why Your Molecular Simulations Might Fail Before They Begin

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One of the most overlooked but absolutely essential steps in setting up a molecular dynamics simulation is Energy Minimization. If you’ve ever wondered why your simulation crashes or produces unstable trajectories, there’s a good chance the culprit lies in skipping…

Quickly Refining NMR Ensembles Without Topology Files

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One common challenge faced by structural biologists working with NMR-derived molecular structures is postprocessing. After initial structure generation with tools like CYANA, converting these NMR ensembles into high-quality, energy-minimized models suitable for publication or molecular design often requires manual setup…

Need to Play a Molecular Path Backwards? Here’s a Simple Approach in SAMSON

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When working with molecular trajectories, it’s often necessary to analyze not just how a system evolves forward, but also what happens when the process is reversed. For instance, in conformational studies or reaction reversibility checks, playing a path backward can…