Author: OneAngstrom

Anyone who uses GROMACS for molecular dynamics simulations knows that managing .mdp files can be time-consuming. These files control the behavior of your simulation, but editing them manually every time you switch between minimization, equilibration, and production phases is error-prone…

When working with protein conformational changes, it’s often necessary not only to generate realistic transitions between structures, but also to save and share these transitions for visualization, analysis, or subsequent simulation. If you’re using SAMSON’s ARAP Interpolator to create smooth…

For molecular modelers, a common challenge is to make quick, interactive changes to a molecular system while a simulation is running—without having to restart the setup process from scratch. In SAMSON, the molecular design platform, this challenge is addressed directly…

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…