SAMSON Blog – Page 36

Using Backgrounds to Strengthen Molecular Presentations in SAMSON

Creating clear and engaging scientific animations for molecular design can be a challenge, especially when you want to convey not only structural information but also guide your audience through a story. One often overlooked aspect that can improve the clarity…

Keeping an Eye on Atoms Without Moving the Camera

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When studying the dynamic behavior of molecules, it’s common to want the camera to stay focused on a certain region — a binding site, an atom group, a functional group in motion — while the rest of the molecular system…

Turning Molecular Simulations into Slides: A Practical Use of the Stop Animation Effect

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Molecular modelers often struggle with one key pain during presentations: controlling the pace of complex animations when explaining key concepts. We’ve all experienced it—you’re presenting a biomolecular simulation, you play through a series of crucial transitions, and your audience gets…

A Simple Way to Show Molecular Disassembly in Your Presentations

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If you’re a molecular modeler preparing visual materials for teaching, a research presentation, or a publication, you’ve likely struggled to clearly communicate the internal architecture of complex molecular assemblies. It’s common to want to highlight specific subunits or depict how…

Quickly show or hide molecular elements using NSL’s presentation attributes

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Molecular modelers often manipulate large, complex systems composed of many structural and visual elements. Whether you’re highlighting specific atoms for analysis or preparing a figure for publication, controlling the visibility of these elements is essential. However, manually toggling visibility through…

Avoid Drifting Ligands: Proper Energy Setup in Ligand Unbinding Simulations

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When exploring ligand unbinding pathways in molecular modeling, one common frustration is the unrealistic movement of either the ligand or the protein during simulations. If you’ve found your protein drifting along with the ligand or noticed unnatural trajectories, the problem…

Tired of Switching Between Tools? Here’s How You Can Integrate Your Workflow in SAMSON

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Molecular modelers often face the challenge of jumping between different tools and platforms to complete different parts of their workflows. Running an optimization in one tool, visualizing it in another, and writing custom scripts to connect them can slow down…

Local GROMACS Simulations Without Slowing Down Your Computer

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Running molecular simulations can be demanding on your computer, especially when using software like GROMACS. If you’ve ever tried to run a local job and found your system nearly unusable during the simulation, you’re not alone. This is a common…

Tired of Losing Molecular Motion Details? Try This Simple Recording Trick

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When creating molecular presentations or simulations, one common frustration among researchers and modelers is realizing that the changes in atomic positions — carefully crafted through movements, docking steps, or simulations — are not thoroughly documented or not reproducible when returning…

Which Unit Cell Should You Choose for Periodic Boundary Conditions?

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When performing molecular simulations with periodic boundary conditions (PBC) in GROMACS, one subtle choice can have a measurable impact on both the accuracy and efficiency of your results: the shape of the unit cell. If you’ve ever wondered whether to…