Author: OneAngstrom

When working with molecular design software, one of the most common challenges is getting started — or getting unstuck. Whether you’re preparing a system for simulation or exploring an unfamiliar interface, the learning curve can slow you down significantly, especially…

Designing new molecules in 3D can often feel overwhelming. Aligning atoms, exploring fragments, checking for clashes — it’s a lot to keep track of in three dimensions. But what if you could start your molecule design in a clean, simplified…

Setting up and running complex molecular simulations can often require a combination of software tools, each with distinct formats, workflows, or interfaces. For molecular modelers, this fragmentation can become a time sink—slowing down exploration and discovery. If you’ve ever thought,…

If you’re a molecular modeler juggling simulations across heavy-duty software like AlphaFold, GROMACS, or NVIDIA BioNeMo services, you’ve probably experienced the headaches of managing multiple jobs: locating results, checking progress, and syncing data across workstations. This can become tedious—especially if…

Finding plausible ligand unbinding pathways in complex protein environments is a critical step in molecular modeling—but it can also be frustrating. Even with sophisticated tools, the system may return incomplete or biologically implausible results. One frequent pain point? The sampling…

Many molecular modelers appreciate having specialized tools for specific simulations, from free energy estimation to advanced visualization techniques. But customizing your environment without wasting time or disrupting your scientific workflow can be a challenge. That’s where SAMSON Connect’s Extension Marketplace…

When working with large biological assemblies in molecular modeling, symmetry can unlock valuable speed-ups and insights. But with size comes ambiguity: large protein complexes often exhibit multiple plausible symmetry groups. If you’ve ever asked yourself “Which symmetry should I use?”,…

For molecular modelers seeking accurate free energy landscapes, Umbrella Sampling remains an essential technique. But before you can compute the Potential of Mean Force (PMF), the often overlooked bottleneck lies in one critical step: selecting meaningful initial conformations from your…