Author: OneAngstrom

For those working in molecular modeling, one common challenge is understanding how computational models translate into actual behavior once simulations are enabled. Did the structural setup contain all necessary parameters? Is the simulation responding as expected when interacting with atoms…

One common frustration when collaborating on molecular design projects is making sure all files stay together — simulation outputs, analysis scripts, papers, images, and custom data often need to be manually tracked and bundled when sharing or switching between machines.…

Creating effective molecular animations can be tricky, especially when you want to illustrate how a molecule becomes structured, how atoms bond progressively, or how a system transitions from disorder to order over time. One frequent challenge is controlling the visibility…

For many molecular modelers and scientists, customizing your molecular design environment is essential. Whether you’re simulating proteins, docking ligands, or running cloud-based structure predictions, adapting your tools to fit your workflow is critical. That’s where SAMSON Extensions come into play.…

When working with complex molecular structures, modelers often need to switch between multiple viewpoints quickly — zooming into a binding site, looking at an overall protein fold, or comparing two conformations side-by-side. This can become time-consuming and repetitive if you…

When working with coarse-grained (CG) systems in GROMACS using the MARTINI force field, one recurring issue for molecular modelers is solvent bead clashes during solvation. These can lead to non-physical behavior during energy minimization or even cause simulations to crash.…

For molecular modelers working with large systems, it’s common to face repetitive and time-consuming tasks like selecting specific atoms based on custom values, geometric patterns, or chemical types. Doing so manually through the interface—especially over thousands of atoms—can become tedious…