Author: OneAngstrom

One of the common challenges in setting up center-of-mass (COM) pulling simulations using GROMACS is defining the correct groups of atoms when default index groups are not sufficient. If you’re dealing with multi-chain molecular systems and want to precisely control…

Presenting molecular structures effectively is often as important as building them. Whether you’re preparing a lecture, visual abstract, or research video, storytelling through molecule animations can engage your audience in ways static images can’t. But one recurring challenge many molecular…

When communicating complex molecular models, visual clarity is essential. However, modelers often face a recurring challenge: how can you guide an audience’s attention to specific components of a system without completely deleting or permanently altering the structure? This is especially…

One of the recurring challenges when setting up molecular dynamics (MD) simulations with GROMACS is defining custom index groups. These groups provide more control during analysis and simulation by letting you specify exactly which atoms or residues you want to…

Designing and modeling DNA origami structures involves multiple tools and file formats, which can make managing and sharing your designs a bit challenging. If you work in DNA nanotechnology and are looking for a more integrated approach, SAMSON may help…

When you’re trying to optimize the properties of a lead compound, exploring small chemical changes at specific sites can be a powerful strategy. Medicinal chemists often want to tweak one part of a molecule and see how it affects activity…

When setting up molecular dynamics simulations with periodic boundary conditions in GROMACS, a common challenge is: how to choose the right simulation box shape. Many users default to cubic cells, but there are smarter options available — especially if you’re…

When presenting molecular models, motion can be a powerful tool to enhance understanding and communication. A static image may capture a single perspective, but animating a molecule—particularly by rotating it—can highlight spatial features, reveal internal organization, and simply make your…