For molecular modelers, reproducibility and optimization of simulations are critical in ensuring accurate results. If you’re a GROMACS user working on specific systems or replicating previous studies, you might find yourself needing to use a specific version of GROMACS that…

Molecular modeling often requires precise and dynamic visualization techniques, especially when exploring complex systems. A common challenge is the need to smoothly navigate the view vertically – moving both the camera’s target point and its position in unison. This is…

When preparing molecular simulations, one common challenge that molecular modelers face is deciding what to do with water molecules, specifically crystal waters. Some of these waters are tightly bound or participate in critical functions in the active site. Others, however,…

Molecular modeling often involves complex structures with numerous atoms and bonds, making visualization a challenge. This is especially true when you want to focus the viewer’s attention on particular elements or demonstrate a molecular process step-by-step. Improper visual clarity can…

Are you working with complex molecular systems and struggling to fine-tune force field parameters? While the Universal Force Field (UFF) is designed to automatically determine atomic types, bonds, and interactions, there are cases where customization becomes vital, especially when dealing…

For molecular modelers, creating visually compelling animations to present findings can often be a daunting task. Whether you’re preparing to demonstrate the results of a docking procedure, emphasize structural insights, or share a molecular journey with your peers, seamless animations…

In molecular modeling, visualizing the dynamics of your designs is often as critical as the design process itself. Understanding when and how to emphasize specific nodes in your molecular models can dramatically improve communication, presentations, and analysis. The ‘Shown’ animation…

Coarse-graining (CG) is a powerful approach to simplify molecular systems, enabling faster simulations by reducing the complexity of all-atom models. If you’re a molecular modeler looking to apply the MARTINI force field, SAMSON’s Martinize2 Extension offers a streamlined workflow for…