SAMSON Blog – Page 324

Running Molecular Dynamics Simulations in the Cloud with GROMACS Wizard

Running molecular dynamics (MD) simulations can be time-consuming and resource-intensive. Many researchers find themselves waiting on local machines for hours — if not days — for simulations to finish. Upgrading local hardware is not always an option, and institutional clusters…

Avoiding Topology Conflicts When Modeling Protein Replicas

OneAngstrom

When setting up coarse-grained molecular dynamics (MD) simulations, many researchers seek to model systems with multiple identical proteins—often for crowding effects, comparative studies, or simulations of assemblies. A common challenge that arises during this workflow is how to correctly prepare…

Quickly Finding Conformations with Many Atoms in SAMSON

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One common task in molecular modeling—especially when working with large molecular datasets or complex simulations—is identifying which conformations meet certain structural criteria. For example, maybe you’re only interested in conformations that contain a large number of atoms. Manually searching through…

Making Sense of Animation Visibility in Molecular Models

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When working on molecular modeling projects involving animations—whether for simulations, presentations, or collaborations with colleagues—clarity and control over what you see and what you don’t are critical. But how do you programmatically control visibility, selection, and naming of animation nodes…

Installing Python Packages in SAMSON Without Leaving the Interface

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For many molecular modelers, scripting in Python has become a core part of their workflow. Whether you’re automating analyses, performing simulations, or applying data science tools, access to Python packages is essential. But managing packages—especially across different environments—can be frustrating.…

Quickly Show or Hide Visual Models in SAMSON with the NSL

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An essential part of working with complex molecular models is managing what you see — and what you don’t. Whether you’re building a model step-by-step, preparing visuals for a publication, or trying to debug a rendering issue, you’ve likely found…

Simplifying Molecular Adjustments: A Closer Look at the Local Move Editor in SAMSON

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Moving specific parts of a molecule precisely can be an everyday hurdle in molecular modeling—especially when you want translational or rotational control along a molecule’s internal, principal directions. Manually adjusting positions or antibody orientations, for example, often feels like moving…

When and Why You Should Minimize Ligands Before Docking

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Ligand preparation is a small but often overlooked step that can create big inconsistencies in molecular docking workflows. If you’re working with a ligand library obtained from public databases or in-house screening efforts, chances are high that those ligands vary…

Why Your Molecular Modeling Work Deserves a Public Profile on SAMSON Connect

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As a molecular modeler, sharing results and building your identity in the research community can be challenging. Email attachments, file transfers, and scattered publication links are common pain points. If you’ve ever felt the frustration of explaining where your latest…

Easier Focus with Pulse: Highlighting Molecular Models with Flow

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When working on complex molecular systems, it’s easy to feel overwhelmed by the sheer number of elements in the scene. Whether you’re visualizing protein interfaces, understanding conformational changes, or creating compelling molecular presentations, sometimes the challenge is simply guiding the…