Author: OneAngstrom

For molecular modelers running simulations with GROMACS in the cloud through the SAMSON GROMACS Wizard, a recurring concern is visibility and control. What happens after submitting a job? How can one monitor progress, pause, or cancel a simulation if something’s…

Molecular modeling often demands very different tools depending on the type of task—a structural biologist, a materials scientist, and a quantum chemist may all use different workflows. This diversity in needs can lead to cluttered or inefficient software environments that…

For molecular modelers working with GROMACS, creating custom index groups can be a valuable but time-consuming step, especially when setting up umbrella sampling or applying restraints to specific parts of a biomolecular system. While GROMACS provides the gmx make_ndx command…

One frequent source of friction for molecular modelers using simulation pipelines is file management—especially when transitioning between sequential steps like energy minimization, NVT, and NPT equilibration. If you’ve ever found yourself wondering whether you picked the right .gro file or…

When working with complex biomolecular systems, understanding the structure of proteins at the residue and chain level is often essential. Whether you’re analyzing experimental data or designing molecular systems, pinpointing features such as conserved regions, mutation sites, or accessible residues…

When sharing molecular animations, it can be hard to clearly indicate when specific atoms or groups appear or disappear. Whether you’re showing a ligand binding event, a reaction intermediate forming, or toggling between two conformational states, your visual message can…

Communicating complex molecular structures often requires more than static images. Whether you’re preparing a conference presentation, teaching molecular biology, or sharing findings with collaborators, clear and compelling animations can make a big difference. One common challenge molecular modelers face is…