Molecular modelers often face challenges in extracting meaningful physical insights from simulation data. One common task is computing the Potential of Mean Force (PMF), a critical quantity for understanding free-energy profiles along reaction coordinates. Achieving this can feel daunting without…

For molecular modelers and researchers working with DNA nanostructures, starting from scratch can feel like reinventing the wheel each time. That’s where tools like Adenita in the SAMSON platform come in handy. Adenita is designed for creating, editing, and exporting…

Analyzing molecular pathways is a fundamental task in molecular modeling, whether you’re studying ligand unbinding events, protein transitions, or reaction coordinates for free energy profiling. But extracting atomic coordinates along these paths can often feel tedious and convoluted. Here’s how…

In molecular modeling and dynamics simulations, creating multiple replicas of a protein system is often necessary, especially when working with coarse-grained models to simulate complex systems. However, for many researchers, this process might feel daunting, as it involves more than…

If you are working on molecular dynamics simulations, you’ve probably encountered the challenge of stabilizing system density after completing the energy minimization and temperature equilibration phases. This phase, known as NPT equilibration, is a crucial step to prepare your system…

Preparing a molecular system for computational simulations often involves a critical step: ensuring electrical neutrality by adding ions to balance the net charge. For molecular modelers working with coarse-grained (CG) systems, this process can be daunting. Fortunately, SAMSON’s GROMACS Wizard…