Author: OneAngstrom

If you’ve ever struggled to communicate molecular processes clearly in your presentations or publications, you’re not alone. A recurring challenge for molecular modelers is making animations that convey structural changes or molecular assemblies in a smooth and visually intuitive way.…

One of the most frequent needs in molecular modeling is geometry optimization—adjusting atomic coordinates in order to find a stable molecular structure. But if you’re used to traditional static methods, you might find the interactive approach in SAMSON both efficient…

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…