Author: OneAngstrom

When creating molecular animations, it’s often essential to trace the movement of atoms over time. Whether you’re demonstrating a docking process, simulating molecular dynamics, or showcasing the motion generated by a custom animation, documenting the precise trajectory can be critical…

When you’re creating a molecular animation in SAMSON, one challenge that can arise—often unexpectedly—is an unwanted change in camera perspective. You might spend a significant amount of time setting up a precise camera orientation for a particular frame, only to…

For molecular modelers, communication often hinges on the clarity and visual impact of shared images. Whether you’re crafting visuals for a publication, presentation, or collaboration, rendering realistic materials can be surprisingly time-consuming. Setting up each surface – glass, metal, or…

When working with complex molecular systems, it’s not always necessary (or desirable) to optimize the whole structure. Whether you’re fine-tuning a ligand inside a binding pocket or just adjusting a fragment of a large biomolecule, minimizing only a specific region…

Working with NMR-derived molecular structures often means handling NOE distance restraints that involve pseudoatoms—averaged positions typically used to represent equivalent hydrogen atoms. While helpful from an experimental perspective, pseudoatoms can become a bottleneck during structure refinement, especially when your modeling…

Visualizing molecular dynamics or conformational changes often means working with complex trajectories. While such motion can reveal critical biological or chemical insights, turning a trajectory into a clear, smooth animation can become a time-consuming task. That’s where SAMSON’s Play path…

Launching molecular dynamics simulations can be time-consuming and demanding on local machines, especially when working with large systems or when you want to stay productive while simulations run. Fortunately, if you’re using SAMSON, there’s a streamlined way to run GROMACS…