For molecular modelers, one major challenge is ensuring that molecular systems are geometrically stable before moving into simulations. This critical step—Energy Minimization—is essential to eliminate steric clashes and optimize the geometry of the system for further molecular dynamics simulations. With…

Why are Simulation Parameters Important? If you’ve ventured into molecular dynamics (MD) simulations, you already know that small parameter tweaks can greatly influence results. Setting the correct simulation parameters is key to ensuring both the accuracy and efficiency of your…

Molecular modeling often involves visualizing complex datasets and structures, but ensuring clarity and precision can be a challenge. This is where the color scheme tools in SAMSON simplify the process, offering a powerful way to enhance the visualization of your…

Umbrella sampling is a powerful technique in molecular simulations for computing the Potential of Mean Force (PMF) along a reaction coordinate. However, setting up the initial conformations and parameters can feel challenging or time-consuming for molecular modelers. Fortunately, the GROMACS…

Creating molecular animations is a cornerstone of molecular modeling and visualization. Often, molecular modelers need a way to showcase atoms and bonds gradually within a structure, either to demonstrate assembly processes, highlight key features, or make presentations smoother. The Reveal…

Molecular modelers face a critical challenge when simulating ligand unbinding pathways: defining a precise and efficient sampling region. The sampling box directly impacts the pathway exploration results, playing a crucial role in ensuring the simulation is both accurate and computationally…

One common pain point for molecular modelers is maintaining a consistent view of a molecular system while working on complex animations or navigating the molecular environment. Changes in the camera’s perspective can disrupt the workflow and make it harder to…