Many molecular modelers—especially students and researchers in institutional environments—face a recurring and frustrating challenge: installing advanced software tools on machines where they don’t have administrative privileges. If you’ve ever been excited to try a new modeling platform, only to be…

Running molecular dynamics simulations can be resource-intensive. If you’ve ever started a GROMACS job only to watch your workstation crawl to a halt—or worse, crash—you’re not alone. For many researchers and students, limited computing power can be a major bottleneck…

Docking simulations are fundamental in molecular modeling, especially in drug design, where one often wants to visualize how ligands interact with receptors. However, presenting these docking events clearly and intuitively can be surprisingly tricky. If you’ve ever struggled to convey…

If you often work with large molecular systems, you’ve likely found yourself repeatedly selecting the same groups of atoms, residues, or molecules. Whether it’s for applying display styles, running simulations, or preparing figures, manually reselecting the same regions adds friction…

If you run molecular dynamics simulations with GROMACS on your local machine, you’ve probably wondered how to get the best performance without overloading your system. The GROMACS Wizard in SAMSON includes a performance settings panel that helps you customize how…

If you’ve ever experienced strange docking results—ligands floating in space, distorted poses, or unrealistic interactions—it might not be a scoring function issue. In many cases, the problem originates from poorly prepared ligand structures. Whether your ligand library comes from a…

When setting up a molecular simulation, small things can save hours down the line. One of those things is organizing your system with custom index groups. GROMACS automatically generates standard index groups like Protein, SOL, and IONS based on the…

Creating effective molecular presentations often requires more than static views. Animations can significantly improve the clarity and engagement of your visualizations. One common requirement researchers face is showcasing a protein, material, or interaction site from multiple angles without overwhelming the…