Author: OneAngstrom

When setting up molecular simulations in GROMACS, automated tools do a great job generating standard index groups (like protein, water, ions). But often, researchers need more control: you might want to monitor a specific subset of amino acids, calculate distances…

Many researchers working with molecular dynamics simulations rely on GROMACS for its performance and flexibility. But one common challenge emerges: how do you integrate a specific version of GROMACS — perhaps compiled with custom flags or needed for reproducibility —…

One of the common tasks in molecular modeling is identifying which atoms or residues are close to one another. This is essential for analyzing interactions, binding pockets, or potential clashes. However, manually browsing molecular structures to find such proximities can…

When working on complex molecular structures in SAMSON, how you see your models can make a real difference. Whether you are analyzing a protein-ligand interaction, presenting your findings, or debugging a simulation, using the appropriate visual model can simplify interpretation…

If you’ve ever tried to manually fine-tune a molecular structure, you know how difficult it can be to predict how atoms should shift when you reposition one of them. Wouldn’t it be helpful if you could visualize forces and relaxations…

When working with protein structures, even small mistakes in backbone conformation can introduce physical strain or mislead simulation outcomes. Before launching into molecular dynamics or interpreting mechanistic insights, it’s helpful to take a moment and check your model’s backbone—especially when…

Energy minimization is one of the most common steps performed in molecular modeling workflows. Whether you’re about to run a molecular dynamics simulation or preparing a system for docking, minimizing the system helps eliminate steric clashes and unrealistic geometries. But…

Setting up coarse-grained (CG) molecular simulations can be rewarding—but also tricky. One of the most common setup issues for newcomers and experienced users alike is related to solvent behavior. CG models, especially those using the popular MARTINI force field, coarse-grain…