For molecular modelers preparing systems for molecular dynamics simulations, a key challenge is achieving accurate thermodynamic conditions before production runs. One critical step in this process is NVT equilibration, which brings the system to the desired temperature while maintaining constant…

Many molecular modelers and computational chemists have their own Python packages—for custom simulations, analysis pipelines, or even neural networks for property prediction. But using them often means jumping between development environments, terminal sessions, and structured molecule viewers. What if everything…

One common challenge in molecular dynamics is ensuring that your system reaches and maintains the desired temperature before you proceed with production simulations. If the temperature isn’t properly stabilized, results can be unreliable or misleading. This is where NVT equilibration…

If you’ve ever worked on complex molecular systems, you’ve likely faced the challenge of jumping between different regions of interest. Whether you need a bird’s-eye view of the entire molecular complex or a close-up on a catalytic site, switching views…

One of the recurring pain points for molecular modelers using GROMACS is managing and fine-tuning molecular dynamics parameters across simulations. Whether you’re running energy minimizations or full production MD simulations, adjusting .mdp files efficiently without making mistakes or interrupting your…

Molecular modelers often juggle numerous molecules when working on simulations, analyses, or comparisons. Switching between them, copying structures, organizing data, and applying operations to specific groups without clutter can be a challenge. This is where Document View in SAMSON becomes…

For many molecular modelers, one significant challenge isn’t running simulations or optimizing structures—it’s presenting their results in a way that is easy to understand. Whether you’re working in research, education, or communication, visual clarity can save time, reduce misinterpretation, and…

One common challenge in preparing biomolecular systems for simulation is managing water molecules. While bulk solvent can be added systematically during solvation, crystal waters—those resolved in the original structure—often have functional roles, especially around the active site of biomolecules. Automatically…