OneAngstrom – Page 114

Making Molecular Models Gradually Appear in SAMSON

When working in molecular modeling, clear visual communication is just as important as robust computational results. For example, when you’re preparing a presentation or video to explain the structure or function of a molecule, it’s important to guide the viewer’s…

From Raw Trajectories to Smooth Transitions: Refining Paths with Parallel NEB in SAMSON

OneAngstrom

In molecular modeling, identifying realistic transition paths between conformational states is often essential—whether you’re exploring ligand unbinding, folding pathways, or chemical reaction mechanisms. Yet, even with tools that generate trajectories, like linear interpolation or sampling-based methods, the paths can be…

A smoother way to switch presentation backgrounds in molecular animations

OneAngstrom

When crafting molecular animations—whether for a research talk, a publication, or a classroom—visual clarity plays a major role. Still, one detail that’s easy to overlook is the transition between visual scenes, especially when presenting sequences with completely different molecular representations,…

Simplifying Molecular Annotations in SAMSON with Note Attributes

OneAngstrom

When managing complex molecular systems in SAMSON, it’s easy to feel overwhelmed by the sheer number of nodes and properties involved. An especially useful—but often overlooked—feature is the ability to annotate structures using Note nodes. These allow users to document…

Running Molecular Dynamics Simulations in the Cloud with GROMACS Wizard

OneAngstrom

Running molecular dynamics (MD) simulations with GROMACS can be resource-intensive, particularly when working with large systems or long time scales. If you’ve ever been limited by computational power on your local machine — or had to abandon simulations partway through…

Why Named Cameras Can Save You Hours in Molecular Modeling Projects

OneAngstrom

When working on complex molecular systems in SAMSON and building dynamic scenes with multiple views, it is not unusual to end up with several camera nodes storing different viewpoints. A common frustration among molecular modelers is locating the right camera…

Two Ways to Add Atoms in SAMSON (and When to Use Each)

OneAngstrom

When you’re building molecular structures from scratch, particularly for custom molecules or intermediates, the process often starts with adding atoms one by one. In SAMSON, there are two primary ways to do this — and both offer distinct benefits depending…

Controlling the Pace of Molecular Animations with Pause Frames

OneAngstrom

When creating molecular animations, one recurring challenge is controlling viewer focus. Things move fast—sometimes too fast. You might be trying to highlight a conformational change, emphasize a binding event, or pause at a molecular interaction that deserves more attention before…

Struggling With GROMACS Index Groups? Here’s a Simple Way to Manage Them Visually

OneAngstrom

Creating and managing index groups in GROMACS can be tedious, especially when working with large biomolecular systems. Whether you’re setting up pulling groups, defining restraints, or preparing simulations, it often requires command-line scripts or careful hand-editing of selections. Fortunately, there’s…

Choosing What to Import After Your NVT Equilibration

OneAngstrom

After running molecular dynamics simulations, especially in tools like the GROMACS Wizard in SAMSON, a common question arises: What exactly should I import from my simulation? This may seem like a simple decision, but it can impact your analysis workflow…