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…
When working on complex molecular systems in SAMSON, we often deal with a multitude of objects: atoms, groups, models, data nodes, and more. Among these, property models define additional data on molecular systems, such as electrostatic potentials, surface properties, or…
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…
When working on complex molecular models in SAMSON, visual clarity can quickly become a challenge. Whether you’re preparing a scene for publication, for collaboration, or simply managing multiple layers of molecular systems, you may find yourself needing to precisely control…
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…
Molecular modelers often work with large, complex systems made up of multiple chains, molecules, and atoms. When managing dense structural data, it can become overwhelming to manually search, select, and manage folders that contain specific types or quantities of atoms.…
