Author: OneAngstrom

Running molecular dynamics simulations often requires significant computational resources — the kind most laptops or even desktops can’t provide for large or long simulations. For many molecular modelers, this turns an exciting project into a frustrating wait. One elegant solution…

For researchers modeling molecular systems involving carbon nanotubes (CNTs), quickly generating realistic nanotube structures is both essential and sometimes surprisingly tedious. Whether you’re running mechanical simulations, building nanochannels, or prototyping NEMS, manually defining chirality vectors or adjusting radii via parameter…

Choosing the right force field is a recurring concern for molecular modelers, especially when dealing with non-standard molecules or specific biochemical conditions. While GROMACS provides several standard force fields, sometimes they just don’t cut it—especially when you need to simulate…

If you’ve ever opened a PDB file and been disappointed to find only part of the structure—just one chain or a fragment of a protein complex—you’re not alone. Many researchers assume PDB files always include the full biological assembly. Instead,…

Designing carbon nanotubes or other tube-like molecular structures has traditionally required a combination of scripting skills, structural chemistry knowledge, and often repetitive modeling steps. If you’re working in nanotechnology, materials science, or molecular modeling, you’ve likely spent time trying to…

When working with complex molecular models, precise alignment becomes critical—especially when comparing structures, preparing input files for simulations, or creating meaningful visualizations. Misaligned structures can lead to errors in analysis, inefficient setups for simulations, and ambiguous visual outputs. Fortunately, SAMSON…

When setting up a GROMACS simulation, you may find yourself needing to analyze a specific portion of a molecular system repeatedly — certain backbone atoms, a ligand, or, for instance, residues forming alpha-helices. In standard GROMACS workflows, this often requires manually…

In molecular modeling, clarity is key—especially when communicating complex structures to a broader audience. Whether you’re preparing a presentation, making educational content, or exploring your designed molecules, visualizing molecular components separately can provide immediate insight into structure-function relationships. This is…

Communicating complex molecular mechanisms often requires more than static images. Whether you’re creating molecular tutorials, preparing research presentations, or simply trying to make your findings clearer to non-specialists, animation can make a real difference. But not all animations are about…

One common obstacle faced by molecular modelers when working with molecular dynamics (MD) simulations is managing input files correctly between simulation stages. If you’ve ever had to rerun an NPT equilibration in GROMACS just because you didn’t set the right…