Author: OneAngstrom

One of the most important steps in running a successful Umbrella Sampling workflow is the definition of the reaction coordinate. This choice will directly impact the relevance and clarity of the computed Potential of Mean Force (PMF) profile. However, selecting…

If you’ve ever struggled to give your molecular presentations more visual impact—or if your audience is tuning out due to lifeless, static shots—this tip is for you. Molecular design platforms like SAMSON offer tools built for clarity and storytelling. One…

Anyone working with molecular simulations using GROMACS has probably encountered the need to define specific groups of atoms—called index groups. Whether for pulling coordinates, selective restraints, or custom analyses, these groups are essential. Yet, editing index.ndx files manually can be…

Imagine you’re working with multiple molecular modeling tools—perhaps you’ve built a workflow using AutoDock Vina for docking studies, a custom Python script for data analysis, and a visualization tool to review results. Keeping everything in sync, managing data flow, and…

Establishing your presence in a scientific platform can be just as essential as conducting the research itself. In fields like molecular modeling and computational chemistry, sharing your work and connections helps promote reproducibility, discoverability, and collaboration. But when it comes…

Building carbon nanotube (CNT) models for simulations or theoretical analysis can often feel like an intimidating task, especially when it involves setting atomic coordinates or chiral vectors manually. Researchers and students alike face the challenge of quickly prototyping different CNT…

Modeling complex molecular systems often requires juggling multiple tools, views, and settings. But all those panels and windows can become overwhelming fast, especially when you’re trying to focus on a specific task like optimizing a conformation or analyzing intermolecular interactions.…