Author: OneAngstrom

When working with structural protein data, it’s common to download a PDB file and start modeling or simulating right away. But sometimes what you see in the asymmetric unit isn’t the whole story. Many biological assemblies involve symmetric arrangements of…

Molecular modelers trying to produce high-quality images for publications, presentations, or communication often face a recurring issue: getting the visuals to look realistic without spending hours tweaking parameters. Representing molecules in photorealistic styles—whether they’re embedded in a glassy matrix, glowing…

Crystals may seem perfect at first glance, but most real-world materials contain defects—small irregularities that can strongly influence a material’s behavior. If you’re involved in molecular modeling of materials and want to explore how imperfections affect crystal structures, SAMSON’s Crystal…

If you’re modeling protein transitions using interpolation techniques like ARAP (As-Rigid-As-Possible), one of the first hurdles is also the most essential: cleaning your input structures. This might seem like a straightforward step, but minor details — unconnected chains, waters, ligands…

When setting up an umbrella sampling simulation, one of the early and critical steps is selecting a proper set of initial conformations. Doing this manually from a trajectory can be tedious and error-prone, especially if you’re unsure how to space…

One of the most common frustrations for molecular modelers running umbrella sampling simulations is deciding on the best way to choose initial conformations. Too sparse, and you lose resolution. Too dense, and computational costs skyrocket. Luckily, the GROMACS Wizard in…

If you’ve tried to build molecular systems with multiple copies of the same protein and coarse-grain them for simulations, you know how small quirks—like repeating chain IDs or overlapping residue indices—can cause big problems later in topology creation or force-field…

One of the most common hurdles when setting up molecular dynamics (MD) simulations is achieving a stable temperature before collecting meaningful data. If you’ve ever encountered temperature drifts or fluctuations in your system, chances are the equilibration phase wasn’t properly…