Author: OneAngstrom

Molecular dynamics (MD) simulations can provide powerful insights into biomolecular behavior at atomic resolution. But running a successful production MD simulation often comes with hurdles: wrong input paths, mismatched parameters, or just extra time spent redoing steps that could have…

Running molecular dynamics (MD) simulations can be time-consuming, particularly when dealing with multiple molecular conformations or systems. For modelers working with repeated simulations, e.g. for different protein structures or multiple poses of a ligand, having to prepare and simulate each…

If you’ve ever worked with multiple protein structures from the Protein Data Bank (PDB), you’ve probably experienced the repetitive – and tedious – process of cleaning them: stripped waters, removed alternate locations, deleted ligands, added missing hydrogens… the list goes…

When setting up molecular dynamics simulations in GROMACS, it’s often useful—if not essential—to define specific groups of atoms for analysis and specialized operations (e.g., as pull groups or monitoring specific domains). These are known as index groups. While GROMACS can…

When presenting complex molecular assemblies, it’s often helpful to clearly show how components fit together. But how do you break apart a molecular complex in a clean, controlled way—without moving every atom manually? This is where the Disassemble animation in…

Molecular modelers often spend a significant amount of time trying to fine-tune how molecular structures are displayed. Whether it’s for better analysis, clearer presentations, or publication-ready visuals, there’s a constant need to control how nanosystems are represented graphically. In SAMSON,…

When preparing molecular animations for presentations or publications, clarity and focus are essential. One of the common challenges molecular modelers face is how to gently de-emphasize or hide specific parts of a model without abruptly removing them. A sudden disappearance…