SAMSON Blog – Page 3

Custom Index Groups: Fine-Tune Your Simulation Setup in SAMSON

When preparing molecular simulations with GROMACS, setting up your system with precision can save you from troubleshooting downstream. One common pain point for molecular modelers, particularly when dealing with analysis or advanced simulation protocols like umbrella sampling and pulling experiments,…

Cleaning Multiple PDB Files Without the Chaos

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Anyone who’s worked with protein structures knows the routine: download a dozen PDB files, clean each one manually, and try not to make mistakes along the way. It’s tedious—and it’s easy to overlook a missing hydrogen or a dangling ion.…

Rewinding Molecular Trajectories: A Closer Look at the ‘Play Reverse Path’ Feature in SAMSON

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When studying molecular systems, a common task is to analyze how a structure evolves over time. Equally essential is the ability to retrace and visualize these changes backwards—whether to better understand conformational transitions, double-check simulations, or prepare smooth looping animations…

Making light nodes appear or disappear in SAMSON with visibility flags

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Molecular modelers working with complex scenes often need to manage multiple light sources to optimize visual renderings. However, coordinating which lights are actually displayed in a rendered view—without deleting or restructuring the scene—can be tricky. What if you just want…

Accessing Academic Benefits in SAMSON: What You Need to Know

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If you’re a researcher, educator, or student working with molecular modeling, minimizing costs while maximizing access to high-quality tools is likely a key concern. SAMSON, the integrative molecular design platform, offers a simple way for academic users to benefit from…

Controlling Molecular Visibility with the ‘Shown’ Animation in SAMSON

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Creating compelling molecular animations often involves more than just rotating models or showing structural transitions. For many molecular modelers, a key challenge is effectively controlling what is visible and when during an animation. Whether you’re assembling a step-by-step enzyme mechanism,…

Getting Precise with Perspectives: Using Dolly Camera Animation in Molecular Design

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When working on complex molecular visualizations, subtle camera movements can make a big difference. Whether you’re constructing a video for a publication, a presentation, or just trying to visually convey a spatial property of your system, camera animations help guide…

Running GROMACS Simulations in the Cloud Without the Headache

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Preparing and running molecular dynamics simulations can be time-consuming and resource-intensive, especially when working with large or complex systems. One common challenge for molecular modelers is limited access to high-performance computing resources, which are often required for extensive GROMACS simulations.…

Avoiding File Errors in GROMACS Wizard: Smarter Input Selection for NVT Equilibration

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One of the common pain points in molecular dynamics workflows is managing input files — especially when moving through simulation steps like energy minimization to equilibration. If you’re using GROMACS Wizard within SAMSON, there’s good news: the platform provides multiple…

A More Precise Way to Edit Molecular Properties in SAMSON

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When building or studying molecular systems, every detail matters — especially when working with atoms, bonds, and residues. Modifying properties like atomic position, element type, or charge for multiple parts of a system can be time-consuming and error-prone if your…