If you’ve ever tried to simulate a system with multiple replicas of the same protein and ran into topology generation errors, you’re not alone. This is a common issue when working with coarse-grained modeling tools like Martinize2 in SAMSON. The…

Many molecular modelers face a recurring challenge when studying functional protein dynamics: how to connect two known conformations of a protein—say, an open and a closed state—with a realistic transition path. This is a critical step for gaining insights into…

When setting up a simulation involving custom pulling forces in GROMACS, one of the first roadblocks many molecular modelers face is the creation of appropriate index groups. These groups are essential to define regions of interest in biomolecular simulations—whether you’re…

Adding motion to molecular simulations can help communicate structural dynamics and emphasize specific interactions. One common need in molecular modeling is showcasing how a group of atoms or residues rotates in 3D space—whether for presenting conformational changes or emphasizing the…

When working on complex molecular systems, modelers often need to switch between different spatial views—zoomed-in interactions, overall structure, or specific orientations. However, changing perspective often means losing track of a previously tuned camera view, and manually restoring it can be…

If you’re working in molecular modeling, you’ve probably been through the painstaking task of sharing files and simulations with collaborators: emailing attachments, using third-party storage platforms, managing access rights manually… not to mention syncing updates across multiple versions of the…

One of the most common points of friction for molecular modelers is efficiently selecting structures—like ligands, residues, or atoms—from large and complex molecular systems. If you’ve ever spent more time than you’d like manually clicking through molecules to highlight regions…