SAMSON Blog – Page 364

Keeping the Essential: Selective Removal of Crystal Waters for GROMACS Simulations

When preparing a molecular system for simulation in GROMACS, one common yet delicate task is handling existing crystal water molecules. While some waters can safely be deleted, others—especially those tightly bound in functional sites—may be crucial to your system’s behavior.…

Pinpoint the Right Molecular Groups: A Practical Look at Node Group Selection in SAMSON

OneAngstrom

When working with complex molecular models, one of the most recurring tasks is selecting the correct subset of structures. Whether you’re isolating a ligand, identifying functional groups, or analyzing a molecular sub-assembly, manual selection is tedious and error-prone. Fortunately, the…

What Does It Really Mean for a Node to Be Hidden in SAMSON?

OneAngstrom

When working with complex molecular systems in SAMSON, controlling what you see—and what you don’t—is essential for clarity and focus. If you’ve ever found yourself wondering why some nodes appear invisible, seemingly at random, you’re not alone. In this post,…

How to Select Negatively Charged Residues in Seconds

OneAngstrom

When working with biomolecular structures, identifying residues with specific properties—like charge—can be a recurring task. Whether you are focusing on the electrostatic interactions, preparing systems for simulation, or simply analyzing subsets of residues, quickly filtering negatively charged amino acids can…

Let Atoms Fade Away to Highlight What Matters

OneAngstrom

When creating molecular animations to educate, explain, or discover, one of the biggest challenges is guiding the viewer’s attention. In complex molecular systems, every atom and bond contributes to visual clutter. But what if you could make selected atoms gently…

Focusing on What Matters: How to Align Specific Protein Regions in SAMSON

OneAngstrom

When comparing protein structures, full-length superposition isn’t always the best approach. What if you’re only interested in a particular domain, motif, or set of residues? Structural noise from the rest of the protein can obscure meaningful insights where you need…

How to Choose Active Atoms with ARAP for Smarter Protein Path Planning

OneAngstrom

When modeling protein conformational changes, efficiency matters. Exploring the full atomistic flexibility of a large biomolecule can be time-consuming and computationally expensive. This is where smart simplification strategies like the As-Rigid-As-Possible (ARAP) method come in handy — especially when using…

Effortless Filtering of Visible Molecular Presentations in SAMSON

OneAngstrom

When working with complex molecular systems in SAMSON, keeping track of what is visible, selected, or hidden can quickly become overwhelming. Especially for users handling layered molecular scenes—such as structures with multiple representations, annotations, or overlays—rapidly filtering and managing displayed…

Why and How to Add Custom Index Groups During GROMACS Equilibration

OneAngstrom

Molecular simulation workflows often demand flexibility, especially when it comes to tracking specific parts of a system. GROMACS users know how critical index groups are—they define atom selections used in restraints, pulling, or analysis. While GROMACS automatically generates common index…

Making Molecular Elements Disappear: A Quick Guide to ‘Hidden’ Animations in SAMSON

OneAngstrom

When creating molecular animations or presentations, one recurring challenge is how to selectively remove elements from view to simplify the message or highlight specific molecular features. Whether you’re presenting a simulation, comparing molecular states, or narrating a process, clear visual…