One of the most common frustrations in molecular modeling is trying to open a file, only to be told that the format is not supported. Whether it’s a .pdb, .xyz, a cryo-EM density file, or something less common, not being…
Precise manipulation of molecular structures is a core task in molecular modeling. Whether you’re preparing models for simulations, visualizations, or comparative studies, structural alignment plays a vital role. Yet, aligning molecules accurately in 3D space can be time-consuming if the…
NPT equilibration is a critical step in molecular dynamics simulations. It’s the phase where your system stabilizes at the desired pressure and density, and skipping or misconfiguring this step can lead to inaccurate results downstream. Fortunately, GROMACS Wizard in SAMSON…
Before diving into modeling the dynamic transitions of proteins, there’s one crucial step that often gets overlooked – correctly preparing your molecular systems. This seemingly simple process can make or break the results you get from advanced tools like the…
One of the ongoing challenges in molecular modeling is making sure protein structures are valid enough for simulation. Protein refinement workflows often reveal residues that don’t quite fit the geometric or energetic expectations—outliers in backbone conformation. These strained residues can…
Running molecular dynamics (MD) simulations can be computationally intensive, especially for large systems. This often limits researchers to what their local hardware can handle, or forces them to navigate complex HPC systems. If you’re a molecular modeler looking for a…
Performing umbrella sampling simulations is a common task in molecular modeling when estimating the Potential of Mean Force (PMF) along a reaction coordinate. But what often frustrates modelers is how cumbersome post-processing can become. Collecting the simulation outputs, ensuring consistency…
When modeling molecules, especially large or complex systems, it’s common to need to optimize only a part of a molecule while keeping the rest fixed. For example, you might want to relax a portion of a ligand while preserving the…
Umbrella Sampling can be a powerful method for exploring free energy landscapes in molecular systems, but before you can run any simulations, you need to decide on something critical: Where should you sample? Choosing the right set of initial conformations…
When preparing molecular presentations—whether for a class, your research group, or funding review panels—maintaining your audience’s attention is critical. A smooth animation can help communicate your data more effectively, but what happens when you need time to say something important…
