Author: OneAngstrom

When preparing coarse-grained (CG) molecular systems using GROMACS, one frequent source of frustration for modelers is unexpected initial clashes or abnormal solvent behavior during equilibration. If you’ve been there — puzzled by poor density or unstable simulations — the issue…

When presenting molecular models to colleagues or during lectures, it can be helpful to integrate context — whether that’s explanatory slides, background visuals, or subtle environmental cues. Yet, switching abruptly between molecular views and background content can feel disjointed. This…

For molecular modelers preparing presentations or videos, one question often arises: how do you clearly communicate the structural complexity of an assembly without overwhelming your audience? Often, the answer lies not in adding more detail — but in temporarily removing…

When you’re putting together a molecular animation in SAMSON, it can be frustrating to get the perfect camera angle on your system… and then lose it. Maybe you adjusted the camera slightly while working, or forgot exactly how you had…

When sharing molecular models or collaborative design files, one common headache is losing associated data—Python scripts, reference images, or experimental datasets often end up scattered across disparate folders or emails. If you’ve ever opened a molecular project only to find…

For molecular modelers working with complex systems, choosing and managing the right computational tools can often feel overwhelming. SAMSON addresses this challenge through its extensibility: you can adapt the platform to your needs by installing Extensions (also known as SAMSON…

When working with molecular systems and running simulations in GROMACS, precise control over the parts of the system you analyze or manipulate can save significant time and prevent errors. One common challenge is the need to define custom index groups…

If you’ve ever recorded a molecular animation in SAMSON only to realize midway that your camera movements are inconsistent or hard to reproduce, you’re not alone. One common challenge in molecular modeling and presentation is crafting smooth, reproducible camera transitions…

When working with molecular models, one frequent challenge scientists face is modifying structures without breaking the simulation pipeline. Whether you want to prototype a new molecule, adjust a ligand, or refine a complex configuration, editing molecular bonds can easily disrupt…