One of the recurring challenges in molecular modeling is ensuring that force field parameters truly reflect the intent behind your molecular system. Whether you’re refining a biomolecule or designing a novel compound, automatic parameterization tools can’t always know exactly what…

When building molecular presentations or animations in SAMSON, there often comes a moment when you wish to record how atoms move—either to show a docking process, a simulation, or a molecular rearrangement. But manually tracking trajectories frame by frame? That’s…

One common source of frustration in molecular dynamics workflows is accidentally using the wrong input file when transitioning between simulation stages. This becomes especially problematic during equilibration steps where mismatches can cause runs to crash or yield incorrect results. In…

Designing nanoscale structures like carbon nanotubes (CNTs) is a common task in nanotechnology and materials science, yet can be time-consuming using traditional modeling tools. One of the most frequent pains reported by molecular modelers is the difficulty in manually assembling…

Designing specific polymer architectures often starts with one fundamental step: defining your own monomers. For molecular modelers working on custom polymers, functionalized scaffolds, or bioconjugates, creating a library of reusable, well-defined repeat units can streamline workflows and minimize errors later…

When molecular modelers simulate complex systems with GROMACS, performance often becomes a bottleneck — especially on local machines. Whether you’re testing a new protocol or running multiple small systems, getting the most out of your processor can make the difference…