Author: OneAngstrom

When setting up a molecular dynamics (MD) simulation involving pulling, a frequent source of frustration among researchers is improper definition of the simulation box. The consequences? Artifacts due to periodic boundary conditions — from nonphysical interactions to misleading energy profiles.…

If you’ve ever run molecular dynamics simulations with GROMACS, you already know how demanding they can be in terms of computational resources. Long trajectories, multiple replicas, and fine-grained time steps can push even powerful workstations to their limits. But what…

It’s a familiar scenario for many molecular modelers preparing visual presentations: you’re building a molecular animation and want specific atoms, molecules, or protein subunits to appear smoothly at a precise point in time. You don’t want them to fade in…

When preparing molecular animations, the clarity of your visuals often plays a key role in how your ideas are received. Whether you’re showing conformational changes, ligand docking, or a molecular mechanism, smooth transitions can greatly enhance viewer comprehension. One common…

For molecular modelers, customizing software to suit specific workflows often means managing a jungle of plugins and add-ons. Whether it’s downloading, installing, updating, or simply keeping track of versions—plugin management can be time-consuming and error-prone. SAMSON provides a different solution…

For many molecular designers and materials scientists, building accurate models of carbon nanotubes (CNTs) often represents a bottleneck in their workflow. Whether you’re simulating transport phenomena, designing sensors, or exploring nanostructured materials, it’s crucial to start with well-defined geometries. But…

When you are studying large macromolecular systems, one notoriously difficult task is to simulate plausible transitions between two known conformations. Whether you’re investigating protein folding, loop dynamics, or viral mechanisms, modeling intermediate structures between an open and closed state can…

Anyone who has worked with GROMACS knows that defining the right index groups can be a challenge—especially when your system involves complex molecular structures or you’re setting up simulations like center-of-mass (COM) pulling. If you’ve ever found yourself tediously creating…