SAMSON Blog – Page 25

How Bond Order Filters Could Save You Hours in Molecular Editing

For molecular modelers and computational chemists, identifying specific types of bonds—like those with fractional bond orders in conjugated systems—can often involve a mix of guesswork and manual inspection. Whether you’re refining a force field, preparing a simulation, or analyzing resonance…

Designing Molecules in 2D While Staying in Sync with 3D

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Designing molecules is one of the central tasks in molecular modeling. But when it comes to building or editing small molecules—especially during early-stage design or cleaning up structures—many scientists still rely on separate 2D sketching tools, later importing their work…

Avoid Common Pitfalls When Setting Up Production MD Simulations

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One challenge that many molecular modelers face with molecular dynamics (MD) simulations is ensuring continuity and consistency between equilibration and production runs. It may sound trivial, but mistakes in setup parameters—particularly when switching from NPT or NVT equilibrations to production—can…

How to Save Time Designing Complex Polymer Sequences

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Designing polymers with custom sequences can be repetitive and tedious, especially when you’re experimenting with variations of monomer units. If you’ve ever found yourself manually repeating patterns or trying to track down bond types between units, there’s a more efficient…

Saving Molecular Structures: What You Need to Know About SAMSON Exporters

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Whether you’re visualizing complex proteins or running simulations on small molecules, it’s likely that at some point you’ll want to save your work in a specific format to share with collaborators, publish your results, or process your data further. That’s…

Smooth Molecular Motion: A Practical Guide to Atom Animation in SAMSON

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When preparing scientific presentations or molecular animations, one common frustration faced by structural biologists and molecular modelers is presenting complex atomic transformations in a clear, smooth, and repeatable way. Often, the motion of molecules is illustrated frame-by-frame, requiring tedious positional…

A Simple Way to Create Custom GROMACS Index Groups in SAMSON

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Adding custom index groups is one of those things that always sounds more complicated than it needs to be. For many GROMACS users, especially those analyzing complex molecular systems or planning umbrella sampling simulations, grouping atoms efficiently is a routine…

Before You Simulate: Why Pre-processing in Molecular Dynamics Matters

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When preparing a molecular system for simulation, it’s tempting to jump straight into running molecular dynamics. But, as every experienced modeler learns, skipping the pre-processing step can lead to frustrating errors or even incorrect results. If you’re using SAMSON with…

Why Only One Editor Can Be Active at a Time in SAMSON

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When working with complex molecular models, it’s easy to get pulled in many directions—building structures, editing geometries, running analyses, visualizing data. With so many tools available in SAMSON, some users wonder why the platform restricts them to using only one…

Making Atoms Appear When You Want Them To

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Molecular animations are a powerful way to explain complex ideas—especially when presenting dynamic molecular processes such as docking, conformational changes, or molecular interactions. However, many researchers and educators struggle with getting things to appear exactly when they want during a…