Author: OneAngstrom

Setting up and running molecular dynamics (MD) simulations can be time-consuming and computationally expensive, especially for large systems or long simulations. Many modelers face hardware limitations on their local machines and end up spending hours managing dependencies or queue systems…

If you’ve ever tried to prepare dozens or even hundreds of protein structures for simulations or machine learning, you know how quickly things can become tedious. Downloading PDB files, stripping water and ions, resolving alternate locations, adding missing atoms… And…

Preparing molecular simulations in GROMACS often involves defining specific atom groups — known as index groups — for tasks like pulling, restraints, or targeted measurements. GROMACS automatically generates standard groups (e.g., for protein, solvent, ions), which often suffice. But sometimes,…

When collaborating with teams or sharing your molecular modeling work with the broader community, how you present yourself online matters just as much as the quality of your research. For users of SAMSON, the integrative molecular design platform, a customizable…

One of the most common setup issues encountered by molecular modelers working on protein-ligand interactions is an incorrect definition of the ligand itself. This can lead to inaccurate path predictions, unexpected energies, and even failure of the algorithm to find…

When analyzing molecular structures and motions, it’s often helpful to step back—literally. While forward trajectories offer valuable insights, playing molecular paths in reverse can highlight subtle interactions, simplify comparisons, or illustrate transitions between conformations more clearly. This is especially useful…

Creating molecular animations can be incredibly powerful when trying to convey structural mechanisms or simulation results — but getting the camera to follow atoms precisely in 3D space is often a challenge. Whether you’re highlighting a docking process or zooming…