Author: OneAngstrom

When fine-tuning a molecular dynamics workflow, being able to define your own atom groups — for pulling, analysis, or restraints — is incredibly important. GROMACS nudges you in the right direction by generating standard index groups automatically, such as Protein,…

When working on optimizing small molecules for better binding affinity or selectivity, one often faces the question: What happens if I replace or attach something at this position? Trial-and-error can be time-consuming, and manual modifications in 3D editors are prone…

When presenting molecular models—whether in research talks, educational content, or collaborative reviews—clarity is key. A common hurdle in visual storytelling is how to draw attention to important structures without cluttering the scene or drowning your audience in static visuals. This…

Specifying the binding site in protein-ligand docking simulations is often one of the most critical — and error-prone — steps in preparing a reliable docking study. Whether you’re working with co-crystalized structures or docking into an apo form, identifying the…

If you’ve ever asked yourself, “Where did my node go?” while working in SAMSON, you’re not alone. Molecular modelers, especially those building complex systems with numerous nested components, often run into confusion when parts of their structure appear to be…

Anyone who has ever built or edited a molecular system knows this familiar moment: the accidental click, the undesired transformation, or the misplaced edit. In complex modeling environments like SAMSON, one changed parameter can ripple through your workflow. That feeling…

When working with complex biomolecular systems, it’s easy to feel overwhelmed by the sheer number of atoms, residues, ligands, and other structural elements. Whether you’re modeling a protein-ligand interaction or preparing a system for simulation, one key challenge is staying…

Building biologically realistic environments around membrane proteins is a regular challenge for molecular modelers. From preparing lipid bilayers to ensuring correct spatial orientation, the process often involves high manual overhead and repetitive trial and error. If you’ve ever struggled with…