Author: OneAngstrom

Communicating molecular insights visually is one of the most powerful ways to convey structure-function relationships, simulation results, or molecular mechanisms. Yet, some subtle visualization choices can make or break the clarity of your output. Have you ever tried to make…

Preparing a coarse-grained (CG) system for molecular dynamics (MD) simulations can often be frustrating when solvent models behave unexpectedly. One common issue many molecular modelers face is improper solvation due to van der Waals (vdW) clash errors or insufficient solvent…

Designing nanoscale systems often requires repeated arrangements of atoms or molecular fragments—think helices, nanotubes, or crystal-like lattices. Yet, replicating and aligning these geometries manually can quickly become tedious and error-prone. That’s where SAMSON’s Pattern Editors come in: intuitive tools that…

Aligning molecular structures in 3D space is a common task in molecular modeling workflows. Whether you’re preparing a system for analysis, visualizing structures together, or setting up simulations, the ability to quickly and accurately align molecules along reference axes or…

When preparing molecular dynamics simulations, researchers often work with multiple starting conformations of the same system. This is especially common in studies involving ligand binding, protein flexibility, or comparative dynamics. However, managing and configuring these conformations for batch simulations can…

One of the challenges molecular modelers often face when working with coarse-grained (CG) molecular dynamics simulations is properly setting up force fields—particularly for MARTINI-based systems. A mismatch in force field parameters can lead to hours of debugging, poor system stability,…

When working with large molecular structures, molecular modelers often face the challenge of isolating specific atoms for inspection or modification. Manually selecting these atoms can be tedious and error-prone—especially in systems with thousands or millions of atoms like biomolecular complexes,…