Author: OneAngstrom

When working with molecular simulations in GROMACS, you often rely on index groups to define subsets of atoms. GROMACS generates standard ones automatically—like protein, water, or ions—but what if you need more control? Whether you’re setting up biased simulations or…

Setting up center-of-mass pulling simulations in GROMACS often requires the definition of custom index groups—particularly when dealing with multi-chain protein systems. For many molecular modelers, this step introduces friction, especially if you’re switching between the command line and visualization tools.…

In molecular modeling, dynamic presentations can help clarify complex mechanisms far better than static images. Whether you’re illustrating a potential drug interaction, conformational change, or even just repositioning molecules to highlight geometry, animations go a long way in explaining scientific…

One of the recurring challenges in molecular presentations is preserving how atoms move during a simulation or an animation. Whether you’re docking molecules, assembling structures, or applying custom motion, understanding and showcasing atomic trajectories is crucial. But what happens when…

Long modeling sessions can strain your eyes, especially when working with highly detailed molecular structures. Many scientists working with digital tools are familiar with this subtle but real discomfort. If you spend hours building, editing, or analyzing molecular models, optimizing…

If you’re a researcher or student working in molecular modeling, you’ve likely experienced the delay—waiting for your IT department to install new scientific software for you because it requires administrator rights. This can slow down your workflow by hours or…

Running molecular dynamics (MD) simulations, especially on large biomolecular systems, often pushes the limits of a researcher’s local hardware. If you’ve ever faced crashes due to memory overload or critical slowdowns on NVT or NPT equilibrations, you’re not alone. This…

One common frustration molecular modelers face when creating animations is trying to zoom into a specific region of a molecular system without altering the focus or perspective too much. Whether preparing a talk, tutorial, or research video, maintaining consistency and…