Author: OneAngstrom

Setting up umbrella sampling simulations can be a daunting task for molecular modelers. From generating reaction coordinates to ensuring proper equilibration across multiple windows, the process contains numerous steps that can quickly become overwhelming. However, SAMSON’s GROMACS Wizard offers a…

Molecular modeling requires precision and efficiency, and molecular modelers often face the challenge of optimizing their workflows or integrating external tools. This is where SAMSON app extensions come in—offering a way to streamline processes, add new functionalities, and make external…

Building complex polymer structures can be a challenging endeavor for molecular modelers. Whether you are designing synthetic polymers, drug-polymer conjugates, or biopolymers, the process often involves intricate workflows, manual adjustments, and lots of trial and error. However, the Polymer Builder…

One of the most crucial steps in Umbrella Sampling is selecting the starting conformations for the umbrella-window simulations. Whether you’re an experienced molecular modeler or just diving into the dynamics of reaction pathways, knowing how to effectively prepare your simulation…

If you’re in the field of molecular modeling and prototyping DNA nanostructures, you’ve likely encountered challenges importing pre-designed DNA origami for reuse or analysis. The DNA origami field is fast-paced, and being able to tap into existing designs is often…

When setting up molecular simulations in GROMACS, the accurate parametrization of ligands is often a challenge, particularly for non-standard molecules. If your ligand isn’t available as a standard residue in your target force field, this step can become particularly daunting.…

Animations can be incredibly valuable in molecular modeling, especially when visualizing complex systems or explaining intricate mechanisms. One common challenge is dynamically highlighting parts of a molecular structure at specific points in your presentation. SAMSON’s Flash animation is specifically designed…

As a molecular modeler working with SAMSON, you may encounter an issue that’s both subtle and frustrating: icons and UI elements appearing uncomfortably small on a high DPI monitor. High resolution monitors are fantastic for clarity, but when applications fail…