Author: OneAngstrom

Running energy minimization jobs using GROMACS in SAMSON can be highly efficient, especially with the user-friendly interface of the GROMACS Wizard. But here’s a common challenge: how do you keep track of your jobs while continuing your work? Molecular modelers…

Presenting molecular structures in a compelling and understandable way can be challenging—especially when sharing models with others who may not be familiar with atomic-level geometry. While static visuals are useful, they often fail to convey spatial relationships and structural details…

In molecular modeling, clarity is key. Whether you’re preparing figures for publication, sharing interactive models, or simply analyzing a complex system, being able to label and annotate atoms, residues, or molecules is essential. However, many users of SAMSON—the integrative molecular…

If you’ve ever performed geometry optimization, you’ve likely faced the challenge of balancing speed and accuracy — especially when working with large structures or when your focus is on relaxing a system before a simulation. One of the lesser-known but…

Visualizing molecular structures clearly and distinctly is central to effective molecular modeling. Whether you’re representing different atom types, residues, domains, or simulation states, your ability to communicate data visually with accuracy and ease can make a significant difference. But here’s…

Color is more than just aesthetics. For molecular modelers, colorization is often key to revealing the underlying story of a structure. Whether you’re inspecting protein stability, analyzing charge distribution, or presenting a clean visual for publication, an effective use of…

When studying molecular mechanisms—such as ligand unbinding or chemical reactions—it’s often not enough to know just the starting and ending molecular structures. Molecular modelers need to understand the transition path a molecule follows between states, particularly through areas around the…

When exploring molecular systems, staying focused on the part of the system that matters most can be surprisingly difficult. Molecules twist, fold, and shift in complex choreography, and during an animation it’s easy to lose sight of the biologically or…