Author: OneAngstrom

Protein structure alignment is a crucial step in molecular modeling, comparative analysis, and drug design. Typically, researchers align entire protein structures to assess similarity, calculate RMSD, or map functional residues. But what if your question is only about a small…

When preparing a coarse-grained (CG) molecular system for simulation, one often encounters a subtle but important issue: solvent placement. If not handled correctly, solvation can result in overlapping CG beads, leading to instability during energy minimization or early MD phases.…

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…