Author: OneAngstrom

When preparing molecular systems for simulations, many researchers overlook a crucial step: neutralizing the system with the proper concentration of ions. This step is simple but can save you hours of troubleshooting down the line when your simulation produces unexpected…

Creating coarse-grained (CG) models is essential for running molecular dynamics simulations efficiently, especially with force fields like MARTINI. But if you’ve ever worked with multiple replicas of a protein structure—say, for studying multimeric interactions or crowded environments—you might have run…

Presenting molecular processes to diverse audiences — from researchers to students — often requires more than static snapshots. Animations play a key role in making molecular simulations more comprehensible and visually intuitive. One common challenge for many molecular modelers is…

When preparing scientific animations for molecular models, showing structural transitions or navigating through large assemblies, how the camera moves across frames can make a substantial difference. Many molecular modelers encounter a recurring challenge: smoothly moving the camera vertically through their…

When preparing biomolecular simulations with GROMACS, molecular modelers often run into a practical challenge: how to define custom index groups that don’t neatly fall into the default categories like protein, solvent, or ions. For example, what if you want to…

When working on molecular systems, small changes can have big consequences. Accidentally deleting an entire chain, misplacing a fragment, or tweaking a parameter too early in the workflow can compromise hours of careful work. What makes it worse is that…

When working with complex molecular systems, molecular modelers often need to alternate between creating, modifying, and analyzing structures. SAMSON provides a modular approach to streamline this workflow through the concept of editors: dedicated tools that let you perform specific interactive…