SAMSON Blog – Page 4

Indexing Beyond the Defaults: Smarter GROMACS Simulations with Custom Groups

Simulation experts using GROMACS often start by relying on automatically generated index groups—like protein, water, or ions. These built-in groups are handy for many standard tasks, but when simulations get more specific (like defining pull groups or focusing on certain…

From Repetition to Pattern: Designing Monomer Sequences with Polymer Builder

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Building custom polymers can quickly become complex—especially when you’re not just connecting one identical monomer after another, but working with patterned sequences. Many computational chemists and molecular designers struggle with modeling repeat units that reflect experimental conditions or functional motifs.…

Filtering Molecular Models by Partial Charge in SAMSON

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When working with complex molecular systems, identifying specific structural groups based on electrostatic properties can be essential. Whether you’re screening ligands, analyzing biomolecular systems, or designing new compounds, partial charges help determine how molecules interact. Yet, combing through thousands of…

Run GROMACS Simulations Without Local Setup: A Quick Look at Cloud Capabilities in SAMSON

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For molecular modelers, running a GROMACS simulation often comes with a big technical prerequisite: installing, compiling, and configuring everything correctly on your local machine. This can take hours—and might involve battling with dependencies, GPU compatibility, or queuing systems. What if…

Avoiding Common Pitfalls in NVT Equilibration: Selecting the Right Input

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Preparing an input structure for NVT Equilibration in molecular modeling can be confusing — especially when working with complex systems or reusing intermediate stages from previous steps. One common frustration among modelers is wrongly selected input files, which can result…

From Conformations to Complete Paths: Optimizing Transition Pathways with NEB in SAMSON

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Understanding how molecular systems transition from one conformation to another is a common challenge in structural biology and molecular modeling. Whether you’re investigating ligand unbinding, protein folding, or allosteric changes, the ability to model transition paths in a reproducible, physically…

Why Your SAMSON Extension Might Not Load (And How to Fix It)

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One of the challenges molecular modelers occasionally face when working with SAMSON is encountering an extension that simply won’t load. It’s frustrating when an Extension you rely on—or have just installed—doesn’t appear in your workspace. But there’s usually a very…

Making Sense of Camera Selection in SAMSON’s Node Specification Language

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When working with complex molecular models in SAMSON, many users take advantage of various node types such as atoms, bonds, groups, and cameras. Cameras play a key role in setting up and reproducing specific viewpoints or visual styles, which is…

Building Carbon Nanotubes by Hand: A Practical Workflow in SAMSON

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Designing carbon nanotubes manually can sound like a daunting challenge—but for molecular modelers needing custom nanotube topologies, it often becomes necessary. Whether you’re tweaking radii, optimizing ring positioning, or exploring non-standard conformations, having hands-on control over nanotube construction is essential.…

Controlling Note Visibility in Molecular Designs: A Simple Way to Stay Organized

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For researchers working with large molecular systems or complex models, visual clarity is critical. As projects grow, molecular modelers often annotate their systems using notes—whether to track hypotheses, mark interaction hotspots, or assist with collaborative storytelling. But as the number…