SAMSON Blog – Page 248

Why Run GROMACS Simulations in the Cloud?

If you’ve ever run molecular dynamics simulations with GROMACS, you already know how demanding they can be in terms of computational resources. Long trajectories, multiple replicas, and fine-grained time steps can push even powerful workstations to their limits. But what…

Making Molecules Appear at Just the Right Moment

OneAngstrom

It’s a familiar scenario for many molecular modelers preparing visual presentations: you’re building a molecular animation and want specific atoms, molecules, or protein subunits to appear smoothly at a precise point in time. You don’t want them to fade in…

Visual Transitions in Molecular Presentations: Adding Background Interpolations

OneAngstrom

When preparing molecular animations, the clarity of your visuals often plays a key role in how your ideas are received. Whether you’re showing conformational changes, ligand docking, or a molecular mechanism, smooth transitions can greatly enhance viewer comprehension. One common…

Tired of Manual Plugins? Here’s How SAMSON Makes Extension Management Easier

OneAngstrom

For molecular modelers, customizing software to suit specific workflows often means managing a jungle of plugins and add-ons. Whether it’s downloading, installing, updating, or simply keeping track of versions—plugin management can be time-consuming and error-prone. SAMSON provides a different solution…

Quickly Generate Carbon Nanotube Models with Precision (No Scripting Needed)

OneAngstrom

For many molecular designers and materials scientists, building accurate models of carbon nanotubes (CNTs) often represents a bottleneck in their workflow. Whether you’re simulating transport phenomena, designing sensors, or exploring nanostructured materials, it’s crucial to start with well-defined geometries. But…

Interpolating Molecular Motions: How to Model Spike Transitions Without Guesswork

OneAngstrom

When you are studying large macromolecular systems, one notoriously difficult task is to simulate plausible transitions between two known conformations. Whether you’re investigating protein folding, loop dynamics, or viral mechanisms, modeling intermediate structures between an open and closed state can…

A Simple Way to Define Custom Index Groups for GROMACS Simulations

OneAngstrom

Anyone who has worked with GROMACS knows that defining the right index groups can be a challenge—especially when your system involves complex molecular structures or you’re setting up simulations like center-of-mass (COM) pulling. If you’ve ever found yourself tediously creating…

Quickly Isolate Property Models Based on Visibility and Selection Flags

OneAngstrom

When working with large molecular systems, molecular modelers often deal with a mix of visual representations, simulation results, and annotations that come from various nodes in the system. Many of these are property models: nodes designed to describe properties (e.g.,…

Easily Find and Filter Notes in Complex Molecular Models

OneAngstrom

When working with detailed molecular models in SAMSON, it’s easy for your workspace to become difficult to navigate. Notes scattered throughout models often contain crucial information—observations, temporary labels, or structural annotations—but they can quickly become visually overwhelming. Thankfully, with the…

Vertical Transitions Made Simple: Pedestal Camera Animation in Molecular Presentations

OneAngstrom

When creating molecular animations, clarity and visual fluency can make or break the message. Whether you’re showcasing ligand binding, structural transitions, or simply guiding your audience through a complex biological environment, how you move the camera matters. But moving the…