Author: OneAngstrom

When running molecular simulations, especially with systems involving complex interactions or assembled components, one common challenge is controlling the movement of specific parts. For example, if you’re simulating a nanorobotic gripper, a poorly configured simulation might result in the gripper…

When working with complex molecular systems, creating compelling and informative visualizations can make interpretation much easier—both for you and for your audience. One common challenge for molecular modelers is how to depict crowded molecular environments in a way that emphasizes…

It’s easy to miss an important detail when visualizing complex molecular motions. As a molecular modeler, you might carefully design animations to demonstrate a docking process, a conformational change, or a molecular assembly—but wouldn’t it be helpful to record the…

Creating coarse-grained (CG) models helps reduce simulation time and computational cost by simplifying atomistic structures. But what if you’re working on systems with multiple protein replicas—for example, repeated units in biological assemblies or membrane-embedded protein clusters? This scenario is common…

A common challenge in setting up molecular simulations with GROMACS is managing selection groups. GROMACS generates standard index groups such as protein, solvent, and ions, but more advanced protocols – from umbrella sampling to pulling and restraints – often require…

Interactive molecular minimization is critical in model refinement, but what if you need to relax only a specific region of a large molecule, without moving the rest? This need frequently arises in structure preparation — whether after adding atoms, modifying…

One common challenge in molecular modeling — especially in nanotechnology, materials science, or biophysics — is replicating complex structural motifs across different geometrical arrangements. Whether you’re trying to build a carbon nanotube, create a crystalline structure, or arrange proteins in…

Reproducibility is a core concern in molecular modeling. Whether you’re publishing results, working with legacy systems, or using specific patches, there are situations where the default GROMACS installation — even the latest one — just won’t do. Fortunately, the GROMACS…

When presenting complex molecular simulations, one of the common challenges is pacing. Animations often move too quickly, not giving viewers enough time to fully observe important transitions, interactions, or structural changes. Whether you’re sharing a ligand binding pathway or a…