If you’ve ever tried generating coarse-grained (CG) molecular models from multi-chain or multi-replica systems, you may have run into a frustrating issue: topology generation fails due to conflicting residue or chain IDs. This is a surprisingly common problem, and unfortunately,…

One common challenge molecular modelers face is sharing or analyzing detailed atom trajectories from ligand unbinding simulations. Whether you’re preparing figures for a publication, comparing alternative pathways, or running further analysis in a third-party tool, having access to the atomic…

When working on nanoscale systems, choosing the right dimensions and structure for a carbon nanotube (CNT) can have a meaningful impact on the behavior of the entire system. But entering these parameters manually over and over, switching between tools, and…

When building molecular models, especially large or branched structures, one of the common frustrations for chemists and molecular designers is accidentally placing fragments too close, overlapping atoms, or misaligning critical functional groups. Even with care, fragment orientation can be tedious…

Creating custom index groups is a key step to increase flexibility and control in molecular simulations with GROMACS. From restraining specific residues to defining pull groups, index files can be crucial. But there’s a common question among SAMSON users who…

Molecular modeling often involves spending long hours analyzing complex structures, adjusting visualization settings, and preparing presentations. For many scientists, particularly those working late or in low-light environments, the bright glare of software interfaces can become tiring and distracting, even leading…

Visualizing molecular motion can be challenging when the part of interest moves rapidly or unpredictably. Adjusting the camera manually to keep focus can be tedious, especially during long animations like molecular dynamics simulations or docking sequences. That’s where the Look…

If you’ve spent time repeatedly coloring atoms, toggling representations, and organizing your molecular scenes, you’re not alone. For many molecular modelers, one of the most frustrating tasks is having to redo the same visualization settings every time they open a…

When preparing molecular presentations or molecular dynamics movies, timing is often everything. A common frustration among researchers and molecular modelers is the abrupt appearance or disappearance of molecular elements, which can be visually jarring or confusing for an audience. If…