Author: OneAngstrom

Understanding how proteins and ligands interact is a core task in molecular modeling, yet many researchers still wrestle with switching between 2D schematic representations and 3D molecular models. Getting the two to match up, remain synchronized, and editable on the…

For molecular modelers working with GROMACS inside SAMSON, customizing molecular dynamics parameters can feel both powerful and a little daunting. Whether you’re fine-tuning your simulation or reusing parameter sets from prior projects, managing .mdp files effectively can save you hours…

When setting up molecular simulations, fine-tuning parameters can be difficult to get right the first time. Whether you’re trying to replicate a consistent energy minimization routine or comparing sets of parameters, remembering what you changed—or worse, losing those carefully adjusted…

Designing molecular systems in motion can be tricky. A frequent challenge molecular modelers face is controlling atom positions while running simulations—especially when certain parts of a nanosystem are meant to stay fixed or move in a strictly defined way. If…

When showcasing molecular designs, attention often gravitates toward the structure itself—protein active sites, molecular interactions, docking configurations. But what happens around the model can be just as important. Backgrounds quietly shape how your audience perceives and understands your work, especially…

When working with molecular systems, one of the most common and repetitive tasks is identifying and selecting atoms of interest. Whether it’s isolating a solvent, highlighting specific residues in a protein, or selecting atoms based on spatial boundaries, this task…

When working with complex molecular systems, one common challenge molecular modelers face is selecting specific atoms according to criteria that go beyond basic clicking or visual inspection. Whether it’s isolating atoms with a certain charge, picking out surface atoms, or…