Author: OneAngstrom

When performing Potential of Mean Force (PMF) calculations, one of the most overlooked yet critical steps is the assessment of histogram coverage. If you’ve ever struggled to understand whether your simulation results are actually telling you the whole story, this…

Anyone who builds molecular systems knows how time-consuming and repetitive it can be to manually duplicate and arrange atomic units in nanoscale patterns. Whether you’re modeling a nanotube, assembling a biomolecular superstructure, or creating a mesoscopic material, controlling the arrangement…

In a world where collaboration in molecular modeling is increasingly international and digital, it matters how easily others can find and connect with you. Whether you’re analyzing protein-ligand interactions, designing materials, or running simulations in the cloud, having a visible—and…

One of the common challenges in molecular modeling is demonstrating how ligands or molecular fragments interact with a receptor in a clear and dynamic way. While molecular docking offers powerful insights, animating these docking events to communicate mechanisms to colleagues…

If you’re involved in molecular modeling, you’ve likely faced this common issue: figuring out how to carry out unfamiliar tasks in a new software tool while staying focused on your research goals. From molecule editing to simulation setup, the learning…

Ever added a label in SAMSON, only to find it mysteriously vanish as you zoom in or out? You’re not alone. Label visibility in SAMSON is a common point of confusion for molecular modelers, especially when preparing clear, informative visualizations…

Creating smooth animations of complex molecular systems can be both powerful and time-consuming. One common challenge molecular modelers face is how to create clean, precise vertical camera motions—especially when communicating structural changes or navigating vertically extended biomolecular assemblies. Whether exploring…

Running molecular simulations with GROMACS requires precision, but it also demands patience—especially when you’re waiting for a system to equilibrate. One of the common challenges researchers face is tracking their simulations while continuing other work. If you’ve ever found yourself…

When working with force fields in molecular modeling, one common challenge is handling systems where automatic perception of atom types and bond orders fails. This can happen during the modeling of new compounds, structures with unconventional bonding, or even systems…