OneAngstrom – Page 79

Avoid Common Errors When Selecting Input Files in NVT Equilibration

One of the subtle yet persistent challenges molecular modelers face during molecular dynamics simulations is input file mismanagement—especially during equilibration steps. When performing NVT Equilibration (constant Number of particles, Volume, Temperature), even a small mistake in choosing the right input…

A Simple Way to Add Rocking Motions to Molecular Presentations

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Creating engaging and informative animations is often a challenge in molecular modeling, especially when trying to convey 3D structures and spatial relationships clearly. One recurring issue modelers face is how to make their molecular presentations more dynamic without overwhelming the…

Managing Scientific Teams in SAMSON: An Easier Way to Collaborate

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When working on complex molecular modeling projects, collaboration becomes not just helpful, but essential. Whether you’re co-authoring papers, sharing protein structures, or running simulations in the cloud, you need a simple and secure way to manage who sees, edits, or…

Making Smarter Selections with Node Group Attributes in SAMSON

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For anyone involved in molecular modeling, especially when working on large systems, selecting and managing groups of atoms, molecules, or molecular subunits efficiently is crucial. Whether you’re editing a protein-ligand complex, analyzing simulation results, or preparing a publication, being able…

Making Molecules Appear Exactly When You Need Them

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When preparing molecular animations, one challenge often faced by researchers and educators is controlling exactly when certain molecules or molecular components become visible in a sequence. Whether you’re highlighting a ligand entering a binding pocket or emphasizing structural reorganization during…

Keeping Track of Cloud Simulations in SAMSON

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Running molecular simulations in the cloud saves time and computational resources—but comes with its own challenges. How can you monitor your progress, retrieve your data, and fine-tune your workflow without a local copy of everything? That’s where the Job Manager…

Filtering Side Chains by Atomic Composition in SAMSON

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When analyzing macromolecular structures, it’s common to focus on particular subsets of residues—like side chains with a certain number of atoms, or ones rich in specific elements. Whether you’re modeling the behavior of hydrophobic patches or analyzing charged environments, being…

Quick Tip: How to Neutralize Your Molecular System (the Right Way)

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When preparing molecular systems for simulations, many researchers overlook a crucial step: neutralizing the system with the proper concentration of ions. This step is simple but can save you hours of troubleshooting down the line when your simulation produces unexpected…

Avoiding Topology Errors When Modeling Protein Replicas in MARTINI

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Creating coarse-grained (CG) models is essential for running molecular dynamics simulations efficiently, especially with force fields like MARTINI. But if you’ve ever worked with multiple replicas of a protein structure—say, for studying multimeric interactions or crowded environments—you might have run…

Making Molecules Appear One Atom at a Time

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Presenting molecular processes to diverse audiences — from researchers to students — often requires more than static snapshots. Animations play a key role in making molecular simulations more comprehensible and visually intuitive. One common challenge for many molecular modelers is…